March 2016 Archives by author

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Starting: Tue Mar 1 00:52:57 CET 2016
Ending: Thu Mar 31 23:26:13 CEST 2016
Messages: 625

[gmx-users] I have a question about 'How h_bond module in Groamcs compute Hydrogen bond correlation function ' 백호용 (자연과학부)
[gmx-users] How Gromacs h_bond module compute hydrogen correlation function ? 백호용 (자연과학부)
[gmx-users] How Gromacs H_bond module compute hydrogen bonding correlation function practically and in detail? 백호용 (자연과학부)
[gmx-users] pull code in 5.1.2 Mark Abraham
[gmx-users] Simulations of non standard nucleic acids Mark Abraham
[gmx-users] Simulations of non standard nucleic acids Mark Abraham
[gmx-users] pull code in 5.1.2 Mark Abraham
[gmx-users] Avoiding Cubic Spline Table non-bonded VdW kernel Mark Abraham
[gmx-users] why .xtc not generated in 5.1.2? Mark Abraham
[gmx-users] Any way to not compute certain interactions? Mark Abraham
[gmx-users] right hand side error Mark Abraham
[gmx-users] Dividing an MD run Mark Abraham
[gmx-users] Pressure of an energy minimized system Mark Abraham
[gmx-users] Pressure of an energy minimized system Mark Abraham
[gmx-users] unit cell vector warning Mark Abraham
[gmx-users] Inconsistent shifts Mark Abraham
[gmx-users] How can I control PME domain decomposition Mark Abraham
[gmx-users] How can I control PME domain decomposition Mark Abraham
[gmx-users] QM/MM error: no such bonded interactions with 5 atoms Mark Abraham
[gmx-users] QM/MM error: no such bonded interactions with 5 atoms Mark Abraham
[gmx-users] Fwd: Trouble with mpirun gmx- 2/2 machines not sharing correctly Mark Abraham
[gmx-users] Building Gromacs 5.1.2 Mark Abraham
[gmx-users] Building Gromacs 5.1.2 Mark Abraham
[gmx-users] Fourier dihedral potential: typo or correct? Mark Abraham
[gmx-users] Fourier dihedral potential: typo or correct? Mark Abraham
[gmx-users] Problem with the mdrun_openmpi on cluster Mark Abraham
[gmx-users] You are applying a switch function to vdw forces or potentials from 0 to 1.2 nm Mark Abraham
[gmx-users] Error in installing Gromacs in Cygwin Mark Abraham
[gmx-users] elastic restraints in MARTINI simulation Mark Abraham
[gmx-users] Dual Xeon workstation - starting one job/cpu Mark Abraham
[gmx-users] elastic restraints in MARTINI simulation Mark Abraham
[gmx-users] elastic restraints in MARTINI simulation Mark Abraham
[gmx-users] convert xtc to ASCII file Mark Abraham
[gmx-users] pressure and potential energy Mark Abraham
[gmx-users] Running Gromacs on clusters Mark Abraham
[gmx-users] Running Gromacs on clusters Mark Abraham
[gmx-users] Query on g_mmpbsa in gromacs Mark Abraham
[gmx-users] Urea induced denaturation and urea force fields. Mark Abraham
[gmx-users] Turn-off the long range Van der Waals interactions Mark Abraham
[gmx-users] Looking for the source of the H-REMD slowdown when decoupling a lot of atoms Mark Abraham
[gmx-users] is it necessary to mdrun posre_npt.mdp first and then posre_nvt.mdp Mark Abraham
[gmx-users] where are the release notes for versions 5.1.1 and 5.1.2? Mark Abraham
[gmx-users] is it necessary to mdrun posre_npt.mdp first and then posre_nvt.mdp Mark Abraham
[gmx-users] is it necessary to mdrun posre_npt.mdp first and then posre_nvt.mdp Mark Abraham
[gmx-users] where are the release notes for versions 5.1.1 and 5.1.2? Mark Abraham
[gmx-users] Suggestion to update online .mdp options for pull code Mark Abraham
[gmx-users] Error: Lost Particles while sorting Mark Abraham
[gmx-users] Error: Lost Particles while sorting Mark Abraham
[gmx-users] grompp protein-ligand complex simulation Adamu, Aliyu
[gmx-users] grompp protein-ligand complex simulation Adamu, Aliyu
[gmx-users] grompp protein-ligand complex simulation Adamu, Aliyu
[gmx-users] right hand side error Albert
[gmx-users] why .xtc not generated in 5.1.2? Albert
[gmx-users] about g_cluster Albert
[gmx-users] pull code in 5.1.2 Alex
[gmx-users] pull code in 5.1.2 Alex
[gmx-users] pull code in 5.1.2 Alex
[gmx-users] IR Spectra Alexander Alexander
[gmx-users] IR Spectra Alexander Alexander
[gmx-users] .mtx file Alexander Alexander
[gmx-users] adding mdp to amber99sb Irem Altan
[gmx-users] adding mdp to amber99sb Irem Altan
[gmx-users] TIP5P - water molecules cannot be settled Irem Altan
[gmx-users] water models Irem Altan
[gmx-users] unit cell vector warning Irem Altan
[gmx-users] TIP5P - water molecules cannot be settled Irem Altan
[gmx-users] TIP5P - water molecules cannot be settled Irem Altan
[gmx-users] water models Irem Altan
[gmx-users] water models Irem Altan
[gmx-users] problem with water models in Gromacs 5.1.2 Irem Altan
[gmx-users] problem with water models in Gromacs 5.1.2 Irem Altan
[gmx-users] TIP5P and crystal waters Irem Altan
[gmx-users] unit cell vector warning Irem Altan
[gmx-users] unit cell vector warning Irem Altan
[gmx-users] unit cell vector warning Irem Altan
[gmx-users] gmx solvate density problem Irem Altan
[gmx-users] -pbc nojump failure Irem Altan
[gmx-users] -pbc nojump failure Irem Altan
[gmx-users] -pbc nojump failure Irem Altan
[gmx-users] -pbc nojump failure Irem Altan
[gmx-users] axial velocity autocorrelation Aranha, Michelle
[gmx-users] adding windows to thermodynamic integration Yoav Atsmon-Raz
[gmx-users] Gromacs DFTB problem Gábor Balogh
[gmx-users] Is simulated annealing mdp ok Mijiddorj Batsaikhan
[gmx-users] Is the any hydrophobic solutions? Mijiddorj Batsaikhan
[gmx-users] Optimal hardware for running Gromacs David Berquist
[gmx-users] on the gromacs force field for keep helix Brett
[gmx-users] 54a7 force field & pdb2gmx & topology database Brett
[gmx-users] a fatal error in step mdrun -v -deffnm em & Brett
[gmx-users] a fatal error in step mdrun -v -deffnm em & Brett
[gmx-users] a fatal error in step mdrun -v -deffnm em & Brett
[gmx-users] pdb2gmx & terminal residues Brett
[gmx-users] pdb2gmx & terminal residues Brett
[gmx-users] pdb2gmx & terminal residues Brett
[gmx-users] pdb2gmx & terminal residues Brett
[gmx-users] a question related to minim.mdp Brett
[gmx-users] Free energy: sum or average VITALY V. CHABAN
[gmx-users] Free energy: sum or average VITALY V. CHABAN
[gmx-users] Rotation of single moleculae in vacuum VITALY V. CHABAN
[gmx-users] -pbc nojump failure Francesco Carbone
[gmx-users] Distance between two specific residues Abid Channa
[gmx-users] Distance between two specific residues Abid Channa
[gmx-users] Distance between two specific residues Abid Channa
[gmx-users] Rmsd Problem Abid Channa
[gmx-users] Rmsd Problem Abid Channa
[gmx-users] Running Gromacs on clusters Ray Chao
[gmx-users] Running Gromacs on clusters Ray Chao
[gmx-users] Regression test 4.6.7 Nicolas Cheron
[gmx-users] Gromacs 5.0 Benchmarking Systems Benjamin Joseph Coscia
[gmx-users] Beginner Question -- Grab Info from Output ANAND AMITKUMAR DHARIA
[gmx-users] How to Set Boundary in Gromacs ANAND AMITKUMAR DHARIA
[gmx-users] Beginner Question -- Grab Info from Output ANAND AMITKUMAR DHARIA
[gmx-users] Volume and boundary Questions ANAND AMITKUMAR DHARIA
[gmx-users] Buckingham Potentials and oplsaa ANAND AMITKUMAR DHARIA
[gmx-users] Can't do parallell free energy calculation with couple_intramol=no -- workaround? Michael Daily
[gmx-users] Can't do parallell free energy calculation with couple_intramol=no -- workaround? Michael Daily
[gmx-users] Can't do parallell free energy calculation with couple_intramol=no -- workaround? Michael Daily
[gmx-users] why .xtc not generated in 5.1.2? João M. Damas
[gmx-users] Postdoctoral opening in biomolecular modeling at IBM Payel Das
[gmx-users] how to run a MD simulation of a tetrameric protein with single stranded DNA having missing bases Pinky Dey
[gmx-users] md of only water - obtaining different pressure in the x , y and z directions Diez Fernandez, Amanda
[gmx-users] grompp protein-ligand complex simulation Christian Bope Domilongo
[gmx-users] Query on g_mmpbsa in gromacs Prasanna Dr
[gmx-users] gromacs.org_gmx-users Digest, Vol 143, Issue 118 Prasanna Dr
[gmx-users] mmpbsa Prasanna Dr
[gmx-users] Membrane Abbas Ebadi
[gmx-users] Dividing an MD run Guillem Prats Ejarque
[gmx-users] Dividing an MD run Guillem Prats Ejarque
[gmx-users] Dividing an MD run Guillem Prats Ejarque
[gmx-users] Dividing an MD run Guillem Prats Ejarque
[gmx-users] Dividing an MD run Guillem Prats Ejarque
[gmx-users] Restart the interrupted program Mahboobeh Eslami
[gmx-users] RMSD plot of the backbone atoms Mahboobeh Eslami
[gmx-users] use of two index group simultaneously Mahboobeh Eslami
[gmx-users] Relative binding free energy Stefania Evoli
[gmx-users] Relative binding free energy Stefania Evoli
[gmx-users] Relative binding free energy Stefania Evoli
[gmx-users] Relative binding free energy Stefania Evoli
[gmx-users] Relative binding free energy Stefania Evoli
[gmx-users] Relative binding free energy Stefania Evoli
[gmx-users] Relative binding free energy Stefania Evoli
[gmx-users] Simulations of non standard nucleic acids Prayagraj Fandilolu
[gmx-users] Steered Molecular Dynamics for citrate channel Bruna Franciele
[gmx-users] Enthalpy and energy questions on a solvated protein Juan José Galano Frutos
[gmx-users] Sulfate ion parameters #SUKRITI GUPTA#
[gmx-users] Umbrella sampling error with drug molecule Khuong Truong Gia
[gmx-users] Binding of a drug to a lipid bilayer using umbrella sampling method Khuong Truong Gia
[gmx-users] Binding of a drug to a lipid bilayer using umbrella sampling method Khuong Truong Gia
[gmx-users] Query about a simple MD with constant electric field Ivan Gladich
[gmx-users] Query about a simple MD with constant electric field Ivan Gladich
[gmx-users] Query about a simple MD with constant electric field Ivan Gladich
[gmx-users] Umbrella sampling along PCA eigenvector using make_edi Hendrik Goeddeke
[gmx-users] color-coding molecule location at different time frame Gaurav Goel
[gmx-users] Meaning of the screen output "largest charge group radii " Agnivo Gosai
[gmx-users] Trajectory correction for pbc before H-bond analysis Agnivo Gosai
[gmx-users] QM/MM error: no such bonded interactions with 5 atoms (Mark Abraham) Groenhof, Gerrit
[gmx-users] Unable to visualize my Polymer chains in VMD software generated using RIS theory in a proper way Abhishek Gupta
[gmx-users] Turn-off the long range Van der Waals interactions Krishna Mohan Gupta
[gmx-users] Turn-off the long range Van der Waals interactions Krishna Mohan Gupta
[gmx-users] Turn-off the long range Van der Waals interactions Krishna Mohan Gupta
[gmx-users] Getting pdb structure Amali Guruge
[gmx-users] Getting pdb structure Amali Guruge
[gmx-users] Protocol for Gromacs analysis João Henriques
[gmx-users] Dividing an MD run João Henriques
[gmx-users] Dividing an MD run João Henriques
[gmx-users] Dividing an MD run João Henriques
[gmx-users] Dividing an MD run João Henriques
[gmx-users] Beginner Question -- Grab Info from Output João Henriques
[gmx-users] gmx analyze (5.1.2) correlation function(s) João Henriques
[gmx-users] gmx analyze (5.1.2) correlation function(s) João Henriques
[gmx-users] Details of 5.0 benchmark report? Adam Huffman
[gmx-users] Any way to not compute certain interactions? Kyle Huston
[gmx-users] Extending the simulation Sun Iba
[gmx-users] Error: not enough memory Sun Iba
[gmx-users] Error: not enough memory Sun Iba
[gmx-users] Error: not enough memory Sun Iba
[gmx-users] Generate diagram/figure with information about protein-ligand interactions Sun Iba
[gmx-users] Error in installing gromacs ISHRAT JAHAN
[gmx-users] tpo is removed.... Mehreen Jan
[gmx-users] tpo is removed after 10ns... help help plz Mehreen Jan
[gmx-users] tpo is removed in simulation Mehreen Jan
[gmx-users] maxh mdrun option does not work with REMD simulation Maud Jusot
[gmx-users] Custom forcefield tutorial? Michał Kadlof
[gmx-users] Own coarse-grained forcefield Michał Kadlof
[gmx-users] simulation a box of water Pradip Kaur
[gmx-users] Warning: you have generated 17732 solvent molecules which are not multiple of 11 . Pradip Kaur
[gmx-users] Warning: you have generated 17732 solvent molecules which are not multiple of 11 . Pradip Kaur
[gmx-users] Warning: you have generated 17732 solvent molecules which are not multiple of 11 . Pradip Kaur
[gmx-users] Warning: you have generated 17732 solvent molecules which are not multiple of 11 . Pradip Kaur
[gmx-users] Warning: you have generated 17732 solvent molecules which are not multiple of 11 . Pradip Kaur
[gmx-users] is it necessary to mdrun posre_npt.mdp first and then posre_nvt.mdp Pradip Kaur
[gmx-users] is it necessary to mdrun posre_npt.mdp first and then posre_nvt.mdp Pradip Kaur
[gmx-users] is it necessary to mdrun posre_npt.mdp first and then posre_nvt.mdp Pradip Kaur
[gmx-users] is it necessary to mdrun posre_npt.mdp first and then posre_nvt.mdp Pradip Kaur
[gmx-users] is it necessary to mdrun posre_npt.mdp first and then posre_nvt.mdp Pradip Kaur
[gmx-users] is it necessary to mdrun posre_npt.mdp first and then posre_nvt.mdp Pradip Kaur
[gmx-users] Urea induced denaturation and urea force fields. Sagar Khavnekar
[gmx-users] Urea induced denaturation and urea force fields. Sagar Khavnekar
[gmx-users] pull code in 5.1.2 Peter Kroon
[gmx-users] Thermostatting in non-equilibrium dynamics Ondrej Kroutil
[gmx-users] Urea induced denaturation and urea force fields. Krzysztof Kuczera
[gmx-users] Optimal hardware for running Gromacs Kutzner, Carsten
[gmx-users] GPU configuration suggestions Kutzner, Carsten
[gmx-users] Umbrella sampling along PCA eigenvector using make_edi Kutzner, Carsten
[gmx-users] adding mdp to amber99sb Justin Lemkul
[gmx-users] Is simulated annealing mdp ok Justin Lemkul
[gmx-users] grompp protein-ligand complex simulation Justin Lemkul
[gmx-users] index file after MD for non bonded interactions Justin Lemkul
[gmx-users] Deuterium order parameter for POPC/POPS mixed lipid bilayer Justin Lemkul
[gmx-users] Constraining hydrogen - heavy atom bonds with different naming. Justin Lemkul
[gmx-users] Constraining hydrogen - heavy atom bonds with different naming. Justin Lemkul
[gmx-users] Constraining hydrogen - heavy atom bonds with different naming. Justin Lemkul
[gmx-users] Membrane Justin Lemkul
[gmx-users] Umbrella sampling error with drug molecule Justin Lemkul
[gmx-users] TIP5P - water molecules cannot be settled Justin Lemkul
[gmx-users] potential energy between 2 energy group Justin Lemkul
[gmx-users] grompp protein-ligand complex simulation Justin Lemkul
[gmx-users] RMSD plot of the backbone atoms Justin Lemkul
[gmx-users] water models Justin Lemkul
[gmx-users] TIP5P - water molecules cannot be settled Justin Lemkul
[gmx-users] TIP5P - water molecules cannot be settled Justin Lemkul
[gmx-users] water models Justin Lemkul
[gmx-users] Dividing an MD run Justin Lemkul
[gmx-users] water models Justin Lemkul
[gmx-users] Dividing an MD run Justin Lemkul
[gmx-users] Dividing an MD run Justin Lemkul
[gmx-users] Different charges in ffnonbonded.itp and aminoacids.rtp files. Justin Lemkul
[gmx-users] use of two index group simultaneously Justin Lemkul
[gmx-users] (no subject) Justin Lemkul
[gmx-users] problem with water models in Gromacs 5.1.2 Justin Lemkul
[gmx-users] Regarding error while generating topology for protein Justin Lemkul
[gmx-users] Neutralizing Justin Lemkul
[gmx-users] distance restraints in mdp Justin Lemkul
[gmx-users] distance restraints in mdp Justin Lemkul
[gmx-users] How the angle/bond length changes during simulation. Justin Lemkul
[gmx-users] Neutralizing Justin Lemkul
[gmx-users] How the angle/bond length changes during simulation. Justin Lemkul
[gmx-users] semi-permeable wall in gromacs Justin Lemkul
[gmx-users] .mtx file Justin Lemkul
[gmx-users] Syntax error - File lig.prm, line 2 Last line read: Justin Lemkul
[gmx-users] semi-permeable wall in gromacs Justin Lemkul
[gmx-users] Regarding using random seed Justin Lemkul
[gmx-users] Regarding energy calculation of head groups Justin Lemkul
[gmx-users] Syntax error - File lig.prm, line 2 Last line read: Justin Lemkul
[gmx-users] Query regarding energy minimization step (step 12: Water molecule starting at atom 13529 can not be settled.) Justin Lemkul
[gmx-users] How to Search Forums and Creating Binary from Existing Topology/Trajectory File Justin Lemkul
[gmx-users] Addendum to Question Justin Lemkul
[gmx-users] problem in editing .eps file of hbond Justin Lemkul
[gmx-users] zero free energy of ligand in water Justin Lemkul
[gmx-users] gmx pdb2gmx for synthetic nucleic acid sequences Justin Lemkul
[gmx-users] tpo is removed.... Justin Lemkul
[gmx-users] Vizualization of lipid protein system Justin Lemkul
[gmx-users] Vizualization of lipid protein system Justin Lemkul
[gmx-users] Problem with the mdrun_openmpi on cluster Justin Lemkul
[gmx-users] Problem with the mdrun_openmpi on cluster Justin Lemkul
[gmx-users] flat-bottom reference file format Justin Lemkul
[gmx-users] Can I fix two of the cubic cell dimensions during an NPT simulation? Justin Lemkul
[gmx-users] The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element Justin Lemkul
[gmx-users] simulation a box of water Justin Lemkul
[gmx-users] simulation a box of water Justin Lemkul
[gmx-users] simulation a box of water Justin Lemkul
[gmx-users] About The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element Justin Lemkul
[gmx-users] The bond in molecular type DPPC between atoms 31 C21 y 32 022 has an estimated oscillational period of 2.1e-02 ps, which is less than 5 times the time step of 1.0e-01 ps Justin Lemkul
[gmx-users] Questions about parameters Justin Lemkul
[gmx-users] Using FFTK generated parameter file for Protein-Ligand simulations Justin Lemkul
[gmx-users] Distance between two specific residues Justin Lemkul
[gmx-users] Warning: you have generated 17732 solvent molecules which are not multiple of 11 . Justin Lemkul
[gmx-users] Custom forcefield tutorial? Justin Lemkul
[gmx-users] umberlla sampling Justin Lemkul
[gmx-users] Domain decomposition error tied to free energy perturbation Justin Lemkul
[gmx-users] gromacs.org_gmx-users Digest, Vol 143, Issue 80 Justin Lemkul
[gmx-users] Inconsistent behavior for bonds involving dummy atoms for alchemical perturbation Justin Lemkul
[gmx-users] Volume and boundary Questions Justin Lemkul
[gmx-users] Temperature dependence of virial of an initial configuration Justin Lemkul
[gmx-users] Questions about parameters Justin Lemkul
[gmx-users] Re :Using FFTK generated parameter file for Protein-Ligand simulations Justin Lemkul
[gmx-users] atomtypes vs atomtypes.atp Justin Lemkul
[gmx-users] lipid bilayer phase transition Justin Lemkul
[gmx-users] lipid bilayer phase transition Justin Lemkul
[gmx-users] semi-permeable wall in gromacs Justin Lemkul
[gmx-users] Tesla K40 vs GeForce GTX TITAN X Justin Lemkul
[gmx-users] color-coding molecule location at different time frame Justin Lemkul
[gmx-users] convert xtc to ASCII file Justin Lemkul
[gmx-users] Inorganic ammonium sulphate with CHARMM force field Justin Lemkul
[gmx-users] About RNA simulation Justin Lemkul
[gmx-users] pressure and potential energy Justin Lemkul
[gmx-users] Ligand breaks during energy minimization Justin Lemkul
[gmx-users] gmx solvate density problem Justin Lemkul
[gmx-users] Getting pdb structure Justin Lemkul
[gmx-users] Ligand breaks during energy minimization Justin Lemkul
[gmx-users] Ligand breaks during energy minimization Justin Lemkul
[gmx-users] Error running simulations with the protein frozen Justin Lemkul
[gmx-users] Error running simulations with the protein frozen Justin Lemkul
[gmx-users] Flat-bottom potential SEGFAULT Justin Lemkul
[gmx-users] Query on g_mmpbsa in gromacs Justin Lemkul
[gmx-users] Binding of a drug to a lipid bilayer using umbrella sampling method Justin Lemkul
[gmx-users] cgenff CTAB Justin Lemkul
[gmx-users] cgenff CTAB Justin Lemkul
[gmx-users] cgenff CTAB Justin Lemkul
[gmx-users] Using CHARMM36 in GROMACS Justin Lemkul
[gmx-users] QM calculation Justin Lemkul
[gmx-users] 54a7 force field & pdb2gmx & topology database Justin Lemkul
[gmx-users] a fatal error in step mdrun -v -deffnm em & Justin Lemkul
[gmx-users] Is the any hydrophobic solutions? Justin Lemkul
[gmx-users] Use pdb file generated with Maestro, in Gromacs Justin Lemkul
[gmx-users] Generate diagram/figure with information about protein-ligand interactions Justin Lemkul
[gmx-users] virtual site - algorithmic reasons Justin Lemkul
[gmx-users] QM calculation Justin Lemkul
[gmx-users] pdb2gmx & terminal residues Justin Lemkul
[gmx-users] Own coarse-grained forcefield Justin Lemkul
[gmx-users] pdb2gmx & terminal residues Justin Lemkul
[gmx-users] pdb2gmx & terminal residues Justin Lemkul
[gmx-users] Relative binding free energy Hannes Loeffler
[gmx-users] Relative binding free energy Hannes Loeffler
[gmx-users] Relative binding free energy Hannes Loeffler
[gmx-users] Relative binding free energy Hannes Loeffler
[gmx-users] Potential energy of each atom Josip Lovrić
[gmx-users] Regarding energy calculation of head groups Raju Lunkad
[gmx-users] Regarding 2D simulation Raju Lunkad
[gmx-users] Use pdb file generated with Maestro, in Gromacs SAKO MIRZAIE
[gmx-users] a fatal error in step mdrun -v -deffnm em & SAKO MIRZAIE
[gmx-users] How to create dual topology to calculate difference in folding free energy due to mutation. SAKO MIRZAIE
[gmx-users] How to create dual topology to calculate difference in folding free energy due to mutation. SAKO MIRZAIE
[gmx-users] How to create dual topology to calculate difference in folding free energy due to mutation. SAKO MIRZAIE
[gmx-users] Query about a simple MD with constant electric field Erik Marklund
[gmx-users] problem in editing .eps file of hbond Erik Marklund
[gmx-users] How Gromacs h_bond module compute hydrogen correlation function ? Erik Marklund
[gmx-users] Trajectory correction for pbc before H-bond analysis Erik Marklund
[gmx-users] How Gromacs h_bond module compute hydrogen correlation function ? Erik Marklund
[gmx-users] Hydrogen bonding pair selection Erik Marklund
[gmx-users] do_dssp problem Erik Marklund
[gmx-users] Getting pdb structure Erik Marklund
[gmx-users] Getting pdb structure Erik Marklund
[gmx-users] Flat-bottom potential SEGFAULT Erik Marklund
[gmx-users] Flat-bottom potential SEGFAULT Erik Marklund
[gmx-users] index file after MD for non bonded interactions Nikhil Maroli
[gmx-users] Extending the simulation Nikhil Maroli
[gmx-users] Syntax error - File lig.prm, line 2 Last line read: Nikhil Maroli
[gmx-users] Syntax error - File lig.prm, line 2 Last line read: Nikhil Maroli
[gmx-users] Syntax error - File lig.prm, line 2 Last line read: Nikhil Maroli
[gmx-users] GPU configuration suggestions Nikhil Maroli
[gmx-users] Error: not enough memory Nikhil Maroli
[gmx-users] Tesla K40 vs GeForce GTX TITAN X Nikhil Maroli
[gmx-users] Rmsd Problem Nikhil Maroli
[gmx-users] Ligand breaks during energy minimization Nikhil Maroli
[gmx-users] Ligand breaks during energy minimization Nikhil Maroli
[gmx-users] water permeations study in channel using Gromacs Nikhil Maroli
[gmx-users] creating representative structures Shyno Mathew
[gmx-users] creating representative structures Shyno Mathew
[gmx-users] convert xtc to ASCII file Athina Meletiou
[gmx-users] output VdW force and electronic static force Zhenyu Meng
[gmx-users] Inconsistent shifts Jan Meyer
[gmx-users] apply force on single molecule Parvez Mh
[gmx-users] Fourier dihedral potential: typo or correct? Parvez Mh
[gmx-users] About The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element Parvez Mh
[gmx-users] The bond in molecular type DPPC between atoms 31 C21 y 32 022 has an estimated oscillational period of 2.1e-02 ps, which is less than 5 times the time step of 1.0e-01 ps Parvez Mh
[gmx-users] atomtypes vs atomtypes.atp Parvez Mh
[gmx-users] About compiling GROMACS by intel compiler Parvez Mh
[gmx-users] About compiling GROMACS by intel compiler Parvez Mh
[gmx-users] Avoiding Cubic Spline Table non-bonded VdW kernel Dave Michael
[gmx-users] GROMACS compilation error on ubuntu 15.10 with OpenCL Josef Mitchell
[gmx-users] potential energy between 2 energy group Tushar Ranjan Moharana
[gmx-users] How to create dual topology to calculate difference in folding free energy due to mutation. Tushar Ranjan Moharana
[gmx-users] How to create dual topology to calculate difference in folding free energy due to mutation. Tushar Ranjan Moharana
[gmx-users] umberlla sampling Ali Mohyeddin
[gmx-users] How to Search Forums and Creating Binary from Existing Topology/Trajectory File Robert Molt
[gmx-users] Addendum to Question Robert Molt
[gmx-users] (no subject) Sepideh Momeninezhad
[gmx-users] query on plotting dynamical quantity Jagannath Mondal
[gmx-users] color-coding molecule location at different time frame Jagannath Mondal
[gmx-users] Number of simulated annealing points Tim Moore
[gmx-users] IR Spectra André Farias de Moura
[gmx-users] IR Spectra André Farias de Moura
[gmx-users] Any way to not compute certain interactions? André Farias de Moura
[gmx-users] md of only water - obtaining different pressure in the x , y and z directions André Farias de Moura
[gmx-users] Inconsistent behavior for bonds involving dummy atoms for alchemical perturbation Ryan Muraglia
[gmx-users] Domain decomposition error tied to free energy perturbation Ryan Muraglia
[gmx-users] Domain decomposition error tied to free energy perturbation Ryan Muraglia
[gmx-users] Minimising forces for vibrational normal mode analysis Nash, Anthony
[gmx-users] Suggestions on running simulations of very long polypeptide chains Nash, Anthony
[gmx-users] Can I fix two of the cubic cell dimensions during an NPT simulation? Nash, Anthony
[gmx-users] Can I fix two of the cubic cell dimensions during an NPT simulation? Nash, Anthony
[gmx-users] pull code for Gromacs 5 Nash, Anthony
[gmx-users] simulation a box of water Saeed Nasiri
[gmx-users] simulation a box of water Saeed Nasiri
[gmx-users] simulation a box of water Saeed Nasiri
[gmx-users] problem in editing .eps file of hbond Shahid Nayeem
[gmx-users] Error in installing Gromacs in Cygwin Shahid Nayeem
[gmx-users] Looking for the source of the H-REMD slowdown when decoupling a lot of atoms Christopher Neale
[gmx-users] where are the release notes for versions 5.1.1 and 5.1.2? Christopher Neale
[gmx-users] *.pdb file for the Tip4p/ice model Christopher Neale
[gmx-users] where are the release notes for versions 5.1.1 and 5.1.2? Christopher Neale
[gmx-users] a question related to minim.mdp Christopher Neale
[gmx-users] Looking for the source of the H-REMD slowdown when decoupling a lot of atoms Christopher Neale
[gmx-users] Suggestion to update online .mdp options for pull code Christopher Neale
[gmx-users] Suggestion to update online .mdp options for pull code Christopher Neale
[gmx-users] Fwd: Trouble with mpirun gmx- 2/2 machines not sharing correctly Jacob Nowatzke
[gmx-users] CPU+GPU nodes required network Amin Nowroozi
[gmx-users] Building Gromacs 5.1.2 Okoroafor, Kelechi
[gmx-users] Building Gromacs 5.1.2 Okoroafor, Kelechi
[gmx-users] Building Gromacs 5.1.2 Okoroafor, Kelechi
[gmx-users] Error with gmx dielectric Roberto Olmi
[gmx-users] Computing dielectric relaxation properties of solutions Roberto Olmi
[gmx-users] Computing dielectric relaxation properties of solutions Roberto Olmi
[gmx-users] Possible bug in g_dielectric and g_dipoles Roberto Olmi
[gmx-users] FEP with position restraints David Fernández Payeras
[gmx-users] elastic restraints in MARTINI simulation Xavier Periole
[gmx-users] Using CHARMM36 in GROMACS Gregory Poon
[gmx-users] Details of 5.0 benchmark report? Szilárd Páll
[gmx-users] Can't do parallell free energy calculation with couple_intramol=no -- workaround? Szilárd Páll
[gmx-users] Fwd: Trouble with mpirun gmx- 2/2 machines not sharing correctly Szilárd Páll
[gmx-users] Free energy: sum or average Szilárd Páll
[gmx-users] Can't do parallell free energy calculation with couple_intramol=no -- workaround? Szilárd Páll
[gmx-users] Problem with the mdrun_openmpi on cluster Szilárd Páll
[gmx-users] gpu-performance reduces during FEP calculation Szilárd Páll
[gmx-users] Optimal hardware for running Gromacs Szilárd Páll
[gmx-users] GROMACS compilation error on ubuntu 15.10 with OpenCL Szilárd Páll
[gmx-users] Looking for the source of the H-REMD slowdown when decoupling a lot of atoms Szilárd Páll
[gmx-users] Suggestion to update online .mdp options for pull code Szilárd Páll
[gmx-users] Error: Lost Particles while sorting Szilárd Páll
[gmx-users] How to perform Essential dynamics sampling and cosine convergence using Gromacs 5.1 Rakesh Ramachandran
[gmx-users] Using FFTK generated parameter file for Protein-Ligand simulations Soumya Lipsa Rath
[gmx-users] gromacs.org_gmx-users Digest, Vol 143, Issue 80 Soumya Lipsa Rath
[gmx-users] Re :Using FFTK generated parameter file for Protein-Ligand simulations Soumya Lipsa Rath
[gmx-users] Ligand breaks during energy minimization Soumya Lipsa Rath
[gmx-users] Ligand breaks during energy minimization Soumya Lipsa Rath
[gmx-users] Ligand breaks during energy minimization Soumya Lipsa Rath
[gmx-users] virtual site - algorithmic reasons Samith Rathnayake
[gmx-users] .mtx file Joaquim Rui de Castro Rodrigues
[gmx-users] save the trajectory Dries Van Rompaey
[gmx-users] distance restraints in mdp Sana Saeed
[gmx-users] gromacs.org_gmx-users Digest, Vol 143, Issue 35 Sana Saeed
[gmx-users] zero free energy of ligand in water Sana Saeed
[gmx-users] LINCS warnings for some lambdas. Sana Saeed
[gmx-users] gromacs.org_gmx-users Digest, Vol 143, Issue 78 Sana Saeed
[gmx-users] area per lipid of POPS/POPC mixed bilayer Catarina A. Carvalheda dos Santos
[gmx-users] Regarding 2D simulation Catarina A. Carvalheda dos Santos
[gmx-users] Neutralizing Parham Jabbarzadeh (Department of Biomedical Science)
[gmx-users] *.pdb file for the Tip4p/ice model Sheelan Sengupta
[gmx-users] *.pdb file for the Tip4p/ice model Sheelan Sengupta
[gmx-users] Pressure of an energy minimized system Rakesh Sharan
[gmx-users] Pressure of an energy minimized system Rakesh Sharan
[gmx-users] Separate lambdas for repulsive and dispersive free energies? Michael Shirts
[gmx-users] Looking for the source of the H-REMD slowdown when decoupling a lot of atoms Michael Shirts
[gmx-users] Looking for the source of the H-REMD slowdown when decoupling a lot of atoms Michael Shirts
[gmx-users] Simulation of the membrane protein using Martini. MDP options Marlon Sidore
[gmx-users] apply force on single molecule Smith, Micholas D.
[gmx-users] Problem with the mdrun_openmpi on cluster Smith, Micholas D.
[gmx-users] Error: Lost Particles while sorting Smith, Micholas D.
[gmx-users] Error: Lost Particles while sorting Smith, Micholas D.
[gmx-users] Error: Lost Particles while sorting Smith, Micholas D.
[gmx-users] Enthalpy and energy questions on a solvated protein David van der Spoel
[gmx-users] Query about a simple MD with constant electric field David van der Spoel
[gmx-users] Potential energy of each atom David van der Spoel
[gmx-users] Computing dielectric relaxation properties of solutions David van der Spoel
[gmx-users] Buckingham Potentials and oplsaa David van der Spoel
[gmx-users] g_sgangle error David van der Spoel
[gmx-users] Parametrization using MARTINI 2.2P force field James Starlight
[gmx-users] Simulation of the membrane protein using Martini. MDP options James Starlight
[gmx-users] Simulation of the membrane protein using Martini. MDP options James Starlight
[gmx-users] Vizualization of lipid protein system James Starlight
[gmx-users] Vizualization of lipid protein system James Starlight
[gmx-users] Vizualization of lipid protein system James Starlight
[gmx-users] Vizualization of lipid protein system James Starlight
[gmx-users] Problem with the mdrun_openmpi on cluster James Starlight
[gmx-users] Problem with the mdrun_openmpi on cluster James Starlight
[gmx-users] Problem with the mdrun_openmpi on cluster James Starlight
[gmx-users] Problem with the mdrun_openmpi on cluster James Starlight
[gmx-users] Problem with the mdrun_openmpi on cluster James Starlight
[gmx-users] Problem with the mdrun_openmpi on cluster James Starlight
[gmx-users] Problem with the mdrun_openmpi on cluster James Starlight
[gmx-users] Problem with the mdrun_openmpi on cluster James Starlight
[gmx-users] Problem with the mdrun_openmpi on cluster James Starlight
[gmx-users] Reconstruction of atomistic details from coarse-grained-structures James Starlight
[gmx-users] Reconstruction of atomistic details from coarse-grained-structures James Starlight
[gmx-users] Reconstruction of atomistic details from coarse-grained-structures James Starlight
[gmx-users] Reconstruction of atomistic details from coarse-grained-structures James Starlight
[gmx-users] Reconstruction of atomistic details from coarse-grained-structures James Starlight
[gmx-users] Reconstruction of atomistic details from coarse-grained-structures James Starlight
[gmx-users] Building dimer system using MARTINI James Starlight
[gmx-users] elastic restraints in MARTINI simulation James Starlight
[gmx-users] elastic restraints in MARTINI simulation James Starlight
[gmx-users] elastic restraints in MARTINI simulation James Starlight
[gmx-users] elastic restraints in MARTINI simulation James Starlight
[gmx-users] Analysis and visualization of CG trajectories James Starlight
[gmx-users] Minimising forces for vibrational normal mode analysis Peter Stern
[gmx-users] Warning: you have generated 17732 solvent molecules which are not multiple of 11 . Peter Stern
[gmx-users] Warning: you have generated 17732 solvent molecules which are not multiple of 11 . Peter Stern
[gmx-users] creating representative structures Téletchéa Stéphane
[gmx-users] GROMOS force field for sphingomyelin and cholesterol Piggot T.
[gmx-users] About compiling GROMACS by intel compiler howie TU
[gmx-users] fix COM Ming Tang
[gmx-users] Verlet and Group lists produce difference charge/voltage distributions Matt Thompson
[gmx-users] flat-bottom reference file format Jinmei Wang
[gmx-users] Error running simulations with the protein frozen Nuo Wang
[gmx-users] Error running simulations with the protein frozen Nuo Wang
[gmx-users] Error running simulations with the protein frozen Nuo Wang
[gmx-users] Separate lambdas for repulsive and dispersive free energies? Nuo Wang
[gmx-users] Separate lambdas for repulsive and dispersive free energies? Nuo Wang
[gmx-users] generating martini-version of lipids Tsjerk Wassenaar
[gmx-users] Membrane Tsjerk Wassenaar
[gmx-users] generating martini-version of lipids Tsjerk Wassenaar
[gmx-users] Protocol for Gromacs analysis Tsjerk Wassenaar
[gmx-users] Protocol for Gromacs analysis Tsjerk Wassenaar
[gmx-users] query on plotting dynamical quantity Tsjerk Wassenaar
[gmx-users] Regarding using random seed Tsjerk Wassenaar
[gmx-users] Regarding using random seed Tsjerk Wassenaar
[gmx-users] Regarding using random seed Tsjerk Wassenaar
[gmx-users] query on plotting dynamical quantity Tsjerk Wassenaar
[gmx-users] Reconstruction of atomistic details from coarse-grained-structures Tsjerk Wassenaar
[gmx-users] creating representative structures Tsjerk Wassenaar
[gmx-users] creating representative structures Tsjerk Wassenaar
[gmx-users] Volume and boundary Questions Tsjerk Wassenaar
[gmx-users] elastic restraints in MARTINI simulation Tsjerk Wassenaar
[gmx-users] elastic restraints in MARTINI simulation Tsjerk Wassenaar
[gmx-users] elastic restraints in MARTINI simulation Tsjerk Wassenaar
[gmx-users] unit cell vector warning Tsjerk Wassenaar
[gmx-users] on the gromacs force field for keep helix Tsjerk Wassenaar
[gmx-users] Use pdb file generated with Maestro, in Gromacs Tsjerk Wassenaar
[gmx-users] -pbc nojump failure Tsjerk Wassenaar
[gmx-users] Generate diagram/figure with information about protein-ligand interactions Tsjerk Wassenaar
[gmx-users] -pbc nojump failure Tsjerk Wassenaar
[gmx-users] how to use gmx rdf to compute the RDF between the COMs of molecules (more than 3) LIANG Xujun
[gmx-users] The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element Poncho Arvayo Zatarain
[gmx-users] The bond in molecular type DPPC between atoms 31 C21 y 32 022 has an estimated oscillational period of 2.1e-02 ps, which is less than 5 times the time step of 1.0e-01 ps Poncho Arvayo Zatarain
[gmx-users] About The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element Poncho Arvayo Zatarain
[gmx-users] You are applying a switch function to vdw forces or potentials from 0 to 1.2 nm Poncho Arvayo Zatarain
[gmx-users] QM/MM error: no such bonded interactions with 5 atoms Roman Zeiss
[gmx-users] QM/MM error: no such bonded interactions with 5 atoms (Mark Abraham) Roman Zeiss
[gmx-users] QMmethod Roman Zeiss
[gmx-users] Infinite DNA periodic boundary conditions Roman Zeiss
[gmx-users] Hydrogen bonding pair selection Binwu Zhao
[gmx-users] Hydrogen bonding pair selection (Erik Marklund) Binwu Zhao
[gmx-users] Dual Xeon workstation - starting one job/cpu Jernej Zidar
[gmx-users] Dual Xeon workstation - starting one job/cpu Jernej Zidar
[gmx-users] Protocol for Gromacs analysis anu chandra
[gmx-users] Protocol for Gromacs analysis anu chandra
[gmx-users] Protocol for Gromacs analysis anu chandra
[gmx-users] Regarding using random seed neha chaudhary
[gmx-users] Regarding using random seed neha chaudhary
[gmx-users] Regarding using random seed neha chaudhary
[gmx-users] Regarding using random seed neha chaudhary
[gmx-users] gmx pdb2gmx for synthetic nucleic acid sequences fulvio ciriaco
[gmx-users] Constraining hydrogen - heavy atom bonds with different naming. Dawid das
[gmx-users] Constraining hydrogen - heavy atom bonds with different naming. Dawid das
[gmx-users] Constraining hydrogen - heavy atom bonds with different naming. Dawid das
[gmx-users] Different charges in ffnonbonded.itp and aminoacids.rtp files. Dawid das
[gmx-users] Different charges in ffnonbonded.itp and aminoacids.rtp files. Dawid das
[gmx-users] How the angle/bond length changes during simulation. Dawid das
[gmx-users] How the angle/bond length changes during simulation. Dawid das
[gmx-users] How the angle/bond length changes during simulation. Dawid das
[gmx-users] semi-permeable wall in gromacs gozde ergin
[gmx-users] semi-permeable wall in gromacs gozde ergin
[gmx-users] semi-permeable wall in gromacs gozde ergin
[gmx-users] semi-permeable wall in gromacs gozde ergin
[gmx-users] Inorganic ammonium sulphate with CHARMM force field gozde ergin
[gmx-users] Reconstruction of atomistic details from coarse-grained-structures carlos.navarro87 at gmail.com
[gmx-users] Reconstruction of atomistic details from coarse-grained-structures carlos.navarro87 at gmail.com
[gmx-users] Reconstruction of atomistic details from coarse-grained-structures carlos.navarro87 at gmail.com
[gmx-users] Generate diagram/figure with information about protein-ligand interactions bio hpc
[gmx-users] Use pdb file generated with Maestro, in Gromacs bio hpc
[gmx-users] Use pdb file generated with Maestro, in Gromacs bio hpc
[gmx-users] Generate diagram/figure with information about protein-ligand interactions bio hpc
[gmx-users] (no subject) joyeuxnoel8
[gmx-users] g_sgangle error pratibha kapoor
[gmx-users] problem in editing .eps file of hbond tasneem kausar
[gmx-users] Error in installing Gromacs in Cygwin tasneem kausar
[gmx-users] Regarding error while generating topology for protein shrikant kaushik
[gmx-users] Query regarding energy minimization step (step 12: Water molecule starting at atom 13529 can not be settled.) shrikant kaushik
[gmx-users] Query regarding energy minimization step (step 12: Water molecule starting at atom 13529 can not be settled.) shrikant kaushik
[gmx-users] Query regarding energy minimization step (step 12: Water molecule starting at atom 13529 can not be settled.) shrikant kaushik
[gmx-users] Questions about parameters abhishek khetan
[gmx-users] Questions about parameters abhishek khetan
[gmx-users] pressure and potential energy abhishek khetan
[gmx-users] pressure and potential energy abhishek khetan
[gmx-users] Query on g_mmpbsa in gromacs rajendra kumar
[gmx-users] Use pdb file generated with Maestro, in Gromacs rajendra kumar
[gmx-users] Embedding a protein into a lipid box using CGMD khourshaeishargh at mech.sharif.ir
[gmx-users] Extend to Embedding a protein into a lipid box using CGMD khourshaeishargh at mech.sharif.ir
[gmx-users] generating martini-version of lipids jagannath mondal
[gmx-users] generating martini-version of lipids jagannath mondal
[gmx-users] query on plotting dynamical quantity jagannath mondal
[gmx-users] gpu-performance reduces during FEP calculation jagannath mondal
[gmx-users] gpu-performance reduces during FEP calculation jagannath mondal
[gmx-users] Extending the simulation jkrieger at mrc-lmb.cam.ac.uk
[gmx-users] Extending the simulation jkrieger at mrc-lmb.cam.ac.uk
[gmx-users] Warning: you have generated 17732 solvent molecules which are not multiple of 11 . jkrieger at mrc-lmb.cam.ac.uk
[gmx-users] You are applying a switch function to vdw forces or potentials from 0 to 1.2 nm jkrieger at mrc-lmb.cam.ac.uk
[gmx-users] Warning: you have generated 17732 solvent molecules which are not multiple of 11 . jkrieger at mrc-lmb.cam.ac.uk
[gmx-users] Warning: you have generated 17732 solvent molecules which are not multiple of 11 . jkrieger at mrc-lmb.cam.ac.uk
[gmx-users] fluxer.py MARTINI shivangi nangia
[gmx-users] Neutralizing mohammad r
[gmx-users] Neutralizing mohammad r
[gmx-users] Neutralizing mohammad r
[gmx-users] Neutralizing mohammad r
[gmx-users] QM calculation mohammad r
[gmx-users] QM calculation mohammad r
[gmx-users] save the trajectory leila salimi
[gmx-users] save the trajectory leila salimi
[gmx-users] mail reg diple moment fluctuation vidhya sankar
[gmx-users] Temperature dependence of virial of an initial configuration rakesh sharan
[gmx-users] Deuterium order parameter for POPC/POPS mixed lipid bilayer kamakshi sikka
[gmx-users] Deuterium order parameter for POPC/POPS mixed lipid bilayer kamakshi sikka
[gmx-users] area per lipid of POPS/POPC mixed bilayer kamakshi sikka
[gmx-users] Extending the simulation sun
[gmx-users] Extending the simulation sun
[gmx-users] Generate diagram/figure with information about protein-ligand interactions sun
[gmx-users] Use pdb file generated with Maestro, in Gromacs sun
[gmx-users] is it necessary to mdrun posre_npt.mdp first and then posre_nvt.mdp sun
[gmx-users] Dividing an MD run badamkhatan togoldor
[gmx-users] do_dssp problem badamkhatan togoldor
[gmx-users] lipid bilayer phase transition xy21hb
[gmx-users] lipid bilayer gel phase simulation xy21hb
[gmx-users] lipid bilayer phase transition xy21hb
[gmx-users] cgenff CTAB xy21hb
[gmx-users] cgenff CTAB xy21hb
[gmx-users] cgenff CTAB xy21hb
[gmx-users] GROMOS force field for sphingomyelin and cholesterol 凌未风
[gmx-users] Potential energy of each atom 张正财
[gmx-users] Potential energy of each atom 张正财
[gmx-users] gromacs.org_gmx-users Digest, Vol 143, Issue 89 张正财
[gmx-users] gmx order index option 李选选
[gmx-users] How can I control PME domain decomposition 柯谱
[gmx-users] About RNA simulation 柳青
[gmx-users] non-bonded function type problem 薛正扬

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