January 2016 Archives by author
Starting: Fri Jan 1 20:17:08 CET 2016
Ending: Sun Jan 31 20:36:11 CET 2016
Messages: 610
- [gmx-users] How to delete Zinc atom from .xtc and .gro files
Hassan Aaryapour
- [gmx-users] How to delete Zinc atom from .xtc and .gro files
Hassan Aaryapour
- [gmx-users] Force-switch algorithm
Mark Abraham
- [gmx-users] Force-switch algorithm
Mark Abraham
- [gmx-users] Cannot write trajectory frame
Mark Abraham
- [gmx-users] Cannot write trajectory frame
Mark Abraham
- [gmx-users] FFTW with AVX
Mark Abraham
- [gmx-users] Force-switch algorithm
Mark Abraham
- [gmx-users] Force-switch algorithm
Mark Abraham
- [gmx-users] Simulation of nonaqueous solvents
Mark Abraham
- [gmx-users] fix simulation box corners NVE
Mark Abraham
- [gmx-users] Force-switch algorithm
Mark Abraham
- [gmx-users] Force-switch algorithm
Mark Abraham
- [gmx-users] Force-switch algorithm
Mark Abraham
- [gmx-users] Problem in Free Energy Calculations
Mark Abraham
- [gmx-users] Force-switch algorithm
Mark Abraham
- [gmx-users] how to adjust the box size to correct density?
Mark Abraham
- [gmx-users] how to adjust the box size to correct density?
Mark Abraham
- [gmx-users] Compilation issues with Gromacs 5.1.1 and SGI MPT
Mark Abraham
- [gmx-users] error using pdb2gmx
Mark Abraham
- [gmx-users] error using pdb2gmx
Mark Abraham
- [gmx-users] Compilation issues with Gromacs 5.1.1 and SGI MPT
Mark Abraham
- [gmx-users] Compilation issues with Gromacs 5.1.1 and SGI MPT
Mark Abraham
- [gmx-users] Compilation issues with Gromacs 5.1.1 and SGI MPT
Mark Abraham
- [gmx-users] preapration of non-standard residue
Mark Abraham
- [gmx-users] Generating topology of 3b68.ent
Mark Abraham
- [gmx-users] Generating topology of 3b68.ent
Mark Abraham
- [gmx-users] membed in mdrun VERSION 5.0.4
Mark Abraham
- [gmx-users] pdb2gmx, chain and segment names in the output pdb
Mark Abraham
- [gmx-users] pdb2gmx, chain and segment names in the output pdb
Mark Abraham
- [gmx-users] problem with do_dssp
Mark Abraham
- [gmx-users] Encountered with error after executing the command "gmx solvate"
Mark Abraham
- [gmx-users] membed in mdrun VERSION 5.0.4
Mark Abraham
- [gmx-users] Launch hybrid MPI/openMP run on multiple nodes
Mark Abraham
- [gmx-users] Simulation terminated after 260 ns of simulation
Mark Abraham
- [gmx-users] Launch hybrid MPI/openMP run on multiple nodes
Mark Abraham
- [gmx-users] tabulated dihedral potential
Mark Abraham
- [gmx-users] custom force constants
Mark Abraham
- [gmx-users] HREMD output
Mark Abraham
- [gmx-users] Not enough memory. Failed to calloc :
Mark Abraham
- [gmx-users] find hbond between different groups during simulation
Mark Abraham
- [gmx-users] Not enough memory. Failed to calloc :
Mark Abraham
- [gmx-users] Not enough memory. Failed to calloc :
Mark Abraham
- [gmx-users] reading tpx file (md_0_1.tpr) version 100 with version 83 program:regenerated tpr problem persist
Mark Abraham
- [gmx-users] reading tpx file (md_0_1.tpr) version 100 with version 83 program:regenerated tpr problem persist
Mark Abraham
- [gmx-users] GPU efficiency
Mark Abraham
- [gmx-users] (no subject)
Mark Abraham
- [gmx-users] Build fails with AVX2_256 on Intel Xeon CPU E5-2680 v3
Mark Abraham
- [gmx-users] Build fails with AVX2_256 on Intel Xeon CPU E5-2680 v3
Mark Abraham
- [gmx-users] Surface tension: output units
Mark Abraham
- [gmx-users] GPU efficiency
Mark Abraham
- [gmx-users] Build fails with AVX2_256 on Intel Xeon CPU E5-2680 v3
Mark Abraham
- [gmx-users] Error in comparison of Coulomb-14 potential?
Mark Abraham
- [gmx-users] Error - syntax
Mark Abraham
- [gmx-users] Temperature Annealing
Mark Abraham
- [gmx-users] Temperature Annealing
Mark Abraham
- [gmx-users] Changing a quantity at each time step using a formula
Mark Abraham
- [gmx-users] Changing a quantity at each time step using a formula
Mark Abraham
- [gmx-users] how to modify the code to generate more controllable checkpoints to restart?
Mark Abraham
- [gmx-users] how to modify the code to generate more controllable checkpoints to restart?
Mark Abraham
- [gmx-users] Simulation runs indefinitely
Mark Abraham
- [gmx-users] Simulation runs indefinitely
Mark Abraham
- [gmx-users] Using Lincs
Mark Abraham
- [gmx-users] error about x of the xxx bonded interactions could not be calculated ....
Mark Abraham
- [gmx-users] error about x of the xxx bonded interactions could not be calculated ....
Mark Abraham
- [gmx-users] error about x of the xxx bonded interactions could not be calculated ....
Mark Abraham
- [gmx-users] adding water with genbox
Mark Abraham
- [gmx-users] Protein-Protein distance
Mark Abraham
- [gmx-users] Protein-Protein distance
Mark Abraham
- [gmx-users] Protein-Protein distance
Mark Abraham
- [gmx-users] Protein-Protein distance
Mark Abraham
- [gmx-users] cgenff script failed
Albert
- [gmx-users] cgenff script failed
Albert
- [gmx-users] GPU efficiency
Albert
- [gmx-users] GPU efficiency
Albert
- [gmx-users] Unusual use for GMX
Alex
- [gmx-users] Constant Potential on Walls of Electrodes
Alex
- [gmx-users] Constant Potential on Walls of Electrodes
Alex
- [gmx-users] doubled atoms
Alex
- [gmx-users] doubled atoms
Alex
- [gmx-users] Energy profile of a single water molecule on Ni surface
Alexander Alexander
- [gmx-users] Energy profile of a single water molecule on Ni surface
Alexander Alexander
- [gmx-users] Energy profile of a single water molecule on Ni surface
Alexander Alexander
- [gmx-users] Heat capacity (C_{v}) for a solid
Alexander Alexander
- [gmx-users] Heat capacity (C_{v}) for a solid
Alexander Alexander
- [gmx-users] Fattal error in gmx dos
Alexander Alexander
- [gmx-users] Fattal error in gmx dos
Alexander Alexander
- [gmx-users] pmf-gwham
Rasha Alqus
- [gmx-users] error using pdb2gmx
Irem Altan
- [gmx-users] error using pdb2gmx
Irem Altan
- [gmx-users] error using pdb2gmx
Irem Altan
- [gmx-users] error using pdb2gmx
Irem Altan
- [gmx-users] error using pdb2gmx
Irem Altan
- [gmx-users] Constraining positions according to B-factors
Irem Altan
- [gmx-users] Constraining positions according to B-factors
Irem Altan
- [gmx-users] Constraining positions according to B-factors
Irem Altan
- [gmx-users] custom force constants
Irem Altan
- [gmx-users] custom force constants
Irem Altan
- [gmx-users] disabling pbc while using trjconv
Irem Altan
- [gmx-users] disabling pbc while using trjconv
Irem Altan
- [gmx-users] adding water with genbox
Irem Altan
- [gmx-users] Pull constrain makes simulation unstable
Michail Palaiokostas Avramidis
- [gmx-users] Pull constrain makes simulation unstable
Michail Palaiokostas Avramidis
- [gmx-users] GROMACS performance with an NVidia Tesla k40c
Michail Palaiokostas Avramidis
- [gmx-users] GROMACS performance with an NVidia Tesla k40c
Michail Palaiokostas Avramidis
- [gmx-users] Force-switch algorithm
Pallavi Banerjee
- [gmx-users] Force-switch algorithm
Pallavi Banerjee
- [gmx-users] Force-switch algorithm
Pallavi Banerjee
- [gmx-users] Force-switch algorithm
Pallavi Banerjee
- [gmx-users] Force-switch algorithm
Pallavi Banerjee
- [gmx-users] Force-switch algorithm
Pallavi Banerjee
- [gmx-users] Regarding Umbrella Sampling Analysis Step
Misa Banno
- [gmx-users] Umbrella Sampling, Analysis Step
Misa Banno
- [gmx-users] Correct method to do Cartesian PCA
Antonio Baptista
- [gmx-users] Connections
Chiara Bello
- [gmx-users] hydrophobic interactions
Chiara Bello
- [gmx-users] problem with do_dssp
Chiara Bello
- [gmx-users] Generating topology of 3b68.ent
Simone Bolognini
- [gmx-users] Generating topology of 3b68.ent
Simone Bolognini
- [gmx-users] Generating topology of 3b68.ent
Simone Bolognini
- [gmx-users] Serine phosphorylation
Simone Bolognini
- [gmx-users] Serine phosphorylation
Simone Bolognini
- [gmx-users] Serine phosphorylation
Simone Bolognini
- [gmx-users] Serine phosphorylation
Simone Bolognini
- [gmx-users] How to fix miising atoms in a pdb file?
Simone Bolognini
- [gmx-users] Gromacs Tutorial
Simone Bolognini
- [gmx-users] g_correlation
Samuel Bowerman
- [gmx-users] Non-Integral Charges
VITALY V. CHABAN
- [gmx-users] viscosity using green kubo relation for ionic liquids
VITALY V. CHABAN
- [gmx-users] genion with Na or Ca
VITALY V. CHABAN
- [gmx-users] how to maintain planarity of graphene sheet
VITALY V. CHABAN
- [gmx-users] g_dipoles_mpi
VITALY V. CHABAN
- [gmx-users] how to maintain planarity of graphene sheet
VITALY V. CHABAN
- [gmx-users] how to maintain planarity of graphene sheet
VITALY V. CHABAN
- [gmx-users] Membrane simulation npt problem
VITALY V. CHABAN
- [gmx-users] Membrane simulation npt problem
VITALY V. CHABAN
- [gmx-users] Energy profile of a single water molecule on Ni surface
VITALY V. CHABAN
- [gmx-users] Surface tension: output units
VITALY V. CHABAN
- [gmx-users] Temperature or Pressure Coupling
VITALY V. CHABAN
- [gmx-users] how to modify the code to generate more controllable checkpoints to restart?
VITALY V. CHABAN
- [gmx-users] how to modify the code to generate more controllable checkpoints to restart?
VITALY V. CHABAN
- [gmx-users] genion with Na or Ca
Turgay Cakmak
- [gmx-users] genion with Na or Ca
Turgay Cakmak
- [gmx-users] Why GROMACS is generating so many output trajectory files?
Elton Carvalho
- [gmx-users] Why GROMACS is generating so many output trajectory files?
Elton Carvalho
- [gmx-users] cut the trajectory in small sub-trajectories
Elton Carvalho
- [gmx-users] Extending job error
Abid Channa
- [gmx-users] Build fails with AVX2_256 on Intel Xeon CPU E5-2680 v3
Nicolas Cheron
- [gmx-users] Build fails with AVX2_256 on Intel Xeon CPU E5-2680 v3
Nicolas Cheron
- [gmx-users] Build fails with AVX2_256 on Intel Xeon CPU E5-2680 v3
Nicolas Cheron
- [gmx-users] split MD trajectory into trajectories of smaller time duration
Sudip Das
- [gmx-users] re-weight Metadynamics trajectory from Plumed to make it canonical ensemble
Christian Bope Domilongo
- [gmx-users] re-weight Metadynamics trajectory from Plumed to make it canonical ensemble
Christian Bope Domilongo
- [gmx-users] re-weight Metadynamics trajectory from Plumed to make it canonical ensemble
Christian Bope Domilongo
- [gmx-users] protein-protein interaction
Mahboobeh Eslami
- [gmx-users] protein-protein interaction
Mahboobeh Eslami
- [gmx-users] free energy calculations
Stefania Evoli
- [gmx-users] relative binding free energy calculation Gromacs 5.0.5
Stefania Evoli
- [gmx-users] Brefeldin A and GDP parameters
Jeremy T First
- [gmx-users] Membrane simulation npt problem
Marco Franzoi
- [gmx-users] Membrane simulation npt problem
Marco Franzoi
- [gmx-users] Membrane simulation npt problem
Marco Franzoi
- [gmx-users] pdb2gmx with GROMOS
Marco Franzoi
- [gmx-users] Serine phosphorylation
Changrong Ge
- [gmx-users] Serine phosphorylation
Changrong Ge
- [gmx-users] Water tutorial
Carmen Di Giovanni
- [gmx-users] How to get a compressed pull force output from SMD simulation ?
Agnivo Gosai
- [gmx-users] MDRUN warning during minimization
Agnivo Gosai
- [gmx-users] Placing water molecules in a defined space in the model
Agnivo Gosai
- [gmx-users] MDRUN warning during minimization
Agnivo Gosai
- [gmx-users] Implementing Gupta potential - different formulism
Gould, Anna
- [gmx-users] Contact_Angles_Calculation
HZJ
- [gmx-users] Contact_Angles_Calculation
HZJ
- [gmx-users] add new atom
Malihe Hasanzadeh
- [gmx-users] new atom
Malihe Hasanzadeh
- [gmx-users] add new residue and new atom
Malihe Hasanzadeh
- [gmx-users] add new residue and new atom
Malihe Hasanzadeh
- [gmx-users] add new residue and new atom
Malihe Hasanzadeh
- [gmx-users] add new residue and new atom
Malihe Hasanzadeh
- [gmx-users] add new residue and new atom
Malihe Hasanzadeh
- [gmx-users] add new residue and new atom
Malihe Hasanzadeh
- [gmx-users] Gromacs Tutorial
João Henriques
- [gmx-users] pdb2gmx, chain and segment names in the output pdb
Maxim Igaev
- [gmx-users] Water tutorial
Maxim Igaev
- [gmx-users] Water tutorial
Maxim Igaev
- [gmx-users] Protein-Protein distance
Life Sciences Inc
- [gmx-users] Protein-Protein distance
Life Sciences Inc
- [gmx-users] Protein-Protein distance
Life Sciences Inc
- [gmx-users] Protein-Protein distance
Life Sciences Inc
- [gmx-users] Protein-Protein distance
Life Sciences Inc
- [gmx-users] Protein-Protein distance
Life Sciences Inc
- [gmx-users] Protein-Protein distance
Life Sciences Inc
- [gmx-users] Protein-Protein distance
Life Sciences Inc
- [gmx-users] How to adjust the box size to correct density?
Chang Woon Jang
- [gmx-users] how to adjust the box size to correct density?
Chang Woon Jang
- [gmx-users] How to adjust the box size to correct density?
Chang Woon Jang
- [gmx-users] How to adjust the box size to correct density?
Chang Woon Jang
- [gmx-users] How to adjust the box size to correct density?
Chang Woon Jang
- [gmx-users] How to adjust the box size to correct density?
Chang Woon Jang
- [gmx-users] how to adjust the box size to correct density?
Chang Woon Jang
- [gmx-users] how to adjust the box size to correct density?
Chang Woon Jang
- [gmx-users] Visualization of conf.gro and confout.gro
Chang Woon Jang
- [gmx-users] Error - syntax
Chang Woon Jang
- [gmx-users] Error - syntax
Chang Woon Jang
- [gmx-users] Error - syntax
Chang Woon Jang
- [gmx-users] error about x of the xxx bonded interactions could not be calculated ....
Chang Woon Jang
- [gmx-users] error about x of the xxx bonded interactions could not be calculated ....
Chang Woon Jang
- [gmx-users] error about x of the xxx bonded interactions could not be calculated ....
Chang Woon Jang
- [gmx-users] Spatial Orientational Correlation Function g(r)
ayşe K
- [gmx-users] g_dipoles_mpi
ayşe K
- [gmx-users] Gromos96 53a6 and Berger Lipids
Kindlein, Moritz
- [gmx-users] Gromos96 53a6 and Berger Lipids
Kindlein, Moritz
- [gmx-users] Issue in Steep descent minimization (Free energy calculation)
Live King
- [gmx-users] Problems in Decoupling LJ Potential
Live King
- [gmx-users] Installation of two versions of Gromacs on one system
Indu Kumari
- [gmx-users] Installation of two versions of Gromacs on one system
Indu Kumari
- [gmx-users] does gromac "mdrun" produce predicted 3d structure?
Arron Lacey
- [gmx-users] does gromac "mdrun" produce predicted 3d structure?
Arron Lacey
- [gmx-users] Force-switch algorithm
Justin Lemkul
- [gmx-users] US perl scripts fails index error
Justin Lemkul
- [gmx-users] Problem using gromacs
Justin Lemkul
- [gmx-users] Problem in Free Energy Calculations
Justin Lemkul
- [gmx-users] Problem in Free Energy Calculations
Justin Lemkul
- [gmx-users] Problem using gromacs
Justin Lemkul
- [gmx-users] Plumed-2.2.0 installation issue
Justin Lemkul
- [gmx-users] Simulation of nonaqueous solvents
Justin Lemkul
- [gmx-users] Scripts to the gromacs
Justin Lemkul
- [gmx-users] Restarting Simulations
Justin Lemkul
- [gmx-users] Force-switch algorithm
Justin Lemkul
- [gmx-users] draw histogram
Justin Lemkul
- [gmx-users] Protein-Protein distance
Justin Lemkul
- [gmx-users] US perl scripts fails index error
Justin Lemkul
- [gmx-users] Problem in Free Energy Calculations
Justin Lemkul
- [gmx-users] umbrella sampling error
Justin Lemkul
- [gmx-users] pbc
Justin Lemkul
- [gmx-users] Simulation of nonaqueous solvents
Justin Lemkul
- [gmx-users] How to adjust the box size to correct density?
Justin Lemkul
- [gmx-users] How to adjust the box size to correct density?
Justin Lemkul
- [gmx-users] How to adjust the box size to correct density?
Justin Lemkul
- [gmx-users] Protein-Protein distance
Justin Lemkul
- [gmx-users] There is no domain decomposition
Justin Lemkul
- [gmx-users] Nvt T-coupling error
Justin Lemkul
- [gmx-users] Regarding value of Elj, Eqq, Clj and Cqq values using LIE Approach
Justin Lemkul
- [gmx-users] Regarding value of Elj, Eqq, Clj and Cqq values using LIE Approach
Justin Lemkul
- [gmx-users] membed in mdrun VERSION 5.0.4
Justin Lemkul
- [gmx-users] Regarding value of Elj, Eqq, Clj and Cqq values using LIE Approach
Justin Lemkul
- [gmx-users] Regarding value of Elj, Eqq, Clj and Cqq values using LIE Approach
Justin Lemkul
- [gmx-users] Connections
Justin Lemkul
- [gmx-users] Visualization of conf.gro and confout.gro
Justin Lemkul
- [gmx-users] Problem in using pdb2gmx to generate top file
Justin Lemkul
- [gmx-users] membed in mdrun VERSION 5.0.4
Justin Lemkul
- [gmx-users] Error while running mdrun with rerun option for LIE calculation
Justin Lemkul
- [gmx-users] How to get a compressed pull force output from SMD simulation ?
Justin Lemkul
- [gmx-users] Error while running mdrun with rerun option for LIE calculation
Justin Lemkul
- [gmx-users] Serine phosphorylation
Justin Lemkul
- [gmx-users] hydrophobic interactions
Justin Lemkul
- [gmx-users] non-bonded parameter
Justin Lemkul
- [gmx-users] non-bond
Justin Lemkul
- [gmx-users] Tau-t should be at least 20 times larger than nsttcouple*dt
Justin Lemkul
- [gmx-users] Pull constrain makes simulation unstable
Justin Lemkul
- [gmx-users] genion with Na or Ca
Justin Lemkul
- [gmx-users] planarity restrain for ligand
Justin Lemkul
- [gmx-users] Non-Integral Charges
Justin Lemkul
- [gmx-users] How to delete Zinc atom from .xtc and .gro files
Justin Lemkul
- [gmx-users] g-membed +KALP in dppc
Justin Lemkul
- [gmx-users] Non-Integral Charges
Justin Lemkul
- [gmx-users] Help for gmx enemat
Justin Lemkul
- [gmx-users] Issue in Steep descent minimization (Free energy calculation)
Justin Lemkul
- [gmx-users] how to maintain planarity of graphene sheet
Justin Lemkul
- [gmx-users] Help for gmx enemat
Justin Lemkul
- [gmx-users] Membrane simulation npt problem
Justin Lemkul
- [gmx-users] temperatures of residues
Justin Lemkul
- [gmx-users] Out of memory error for g_density and trjconv
Justin Lemkul
- [gmx-users] temperatures of residues
Justin Lemkul
- [gmx-users] Membrane simulation npt problem
Justin Lemkul
- [gmx-users] Alkane parameters for charm forcefield on gromacs
Justin Lemkul
- [gmx-users] cgenff script failed
Justin Lemkul
- [gmx-users] Alkane parameters for charm forcefield on gromacs
Justin Lemkul
- [gmx-users] Extending job error
Justin Lemkul
- [gmx-users] pdb2gmx with GROMOS
Justin Lemkul
- [gmx-users] pdb2gmx with GROMOS
Justin Lemkul
- [gmx-users] find hbond between different groups during simulation
Justin Lemkul
- [gmx-users] Error estimate for order parameter
Justin Lemkul
- [gmx-users] Not enough memory. Failed to calloc :
Justin Lemkul
- [gmx-users] find hbond between different groups during simulation
Justin Lemkul
- [gmx-users] Constraints errors
Justin Lemkul
- [gmx-users] Error bar of order parameter
Justin Lemkul
- [gmx-users] Error bar of order parameter
Justin Lemkul
- [gmx-users] Error bar
Justin Lemkul
- [gmx-users] trivial question about water molecules
Justin Lemkul
- [gmx-users] trivial question about water molecules
Justin Lemkul
- [gmx-users] does gromac "mdrun" produce predicted 3d structure?
Justin Lemkul
- [gmx-users] does gromac "mdrun" produce predicted 3d structure?
Justin Lemkul
- [gmx-users] Topology for Sphingomyelin
Justin Lemkul
- [gmx-users] A question about pressure coupling and random seed generator in microsecond long simulations
Justin Lemkul
- [gmx-users] gromacs.org_gmx-users Digest, Vol 141, Issue 93
Justin Lemkul
- [gmx-users] Topology for Sphingomyelin
Justin Lemkul
- [gmx-users] Problem with DHT residue not found.
Justin Lemkul
- [gmx-users] Energy profile of a single water molecule on Ni surface
Justin Lemkul
- [gmx-users] Energy profile of a single water molecule on Ni surface
Justin Lemkul
- [gmx-users] Energy profile of a single water molecule on Ni surface
Justin Lemkul
- [gmx-users] reading tpx file (md_0_1.tpr) version 100 with version 83 program:regenerated tpr problem persist
Justin Lemkul
- [gmx-users] reading tpx file (md_0_1.tpr) version 100 with version 83 program:regenerated tpr problem persist
Justin Lemkul
- [gmx-users] Query on Protein-ligand interaction energy calculation
Justin Lemkul
- [gmx-users] MDRUN warning during minimization
Justin Lemkul
- [gmx-users] Temperature Annealing
Justin Lemkul
- [gmx-users] Error - syntax
Justin Lemkul
- [gmx-users] Temperature Annealing
Justin Lemkul
- [gmx-users] Temperature Annealing
Justin Lemkul
- [gmx-users] Deuterium order parameter for DPPC
Justin Lemkul
- [gmx-users] Question
Justin Lemkul
- [gmx-users] Placing water molecules in a defined space in the model
Justin Lemkul
- [gmx-users] Deuterium order parameter for DPPC
Justin Lemkul
- [gmx-users] MDRUN warning during minimization
Justin Lemkul
- [gmx-users] Using Lincs
Justin Lemkul
- [gmx-users] Simulation runs indefinitely
Justin Lemkul
- [gmx-users] High temperature simulation with GROMOS96 54a7
Justin Lemkul
- [gmx-users] Water tutorial
Justin Lemkul
- [gmx-users] Definition of mol_cog
Justin Lemkul
- [gmx-users] Define custom moltype for free energy calculations
Justin Lemkul
- [gmx-users] protein-protein interaction
Justin Lemkul
- [gmx-users] add new atom
Justin Lemkul
- [gmx-users] metal-surfactant ligand topology
Justin Lemkul
- [gmx-users] free energy calculations
Justin Lemkul
- [gmx-users] (no subject)
Justin Lemkul
- [gmx-users] add new residue and new atom
Justin Lemkul
- [gmx-users] (no subject)
Justin Lemkul
- [gmx-users] add new residue and new atom
Justin Lemkul
- [gmx-users] add new residue and new atom
Justin Lemkul
- [gmx-users] add new residue and new atom
Justin Lemkul
- [gmx-users] adding water with genbox
Justin Lemkul
- [gmx-users] Fattal error in gmx dos
Justin Lemkul
- [gmx-users] Fattal error in gmx dos
Justin Lemkul
- [gmx-users] freeze group in NPT ensemble in gromacs 5.x
Justin Lemkul
- [gmx-users] add new residue and new atom
Justin Lemkul
- [gmx-users] gmx sasa
Justin Lemkul
- [gmx-users] Definition of mol_cog
Xingcheng Lin
- [gmx-users] Correct method to do Cartesian PCA
Bin Liu
- [gmx-users] Correct method to do Cartesian PCA
Bin Liu
- [gmx-users] Correct method to do Cartesian PCA
Bin Liu
- [gmx-users] Vesicle simulation crashed with dry martini force field
Shule Liu
- [gmx-users] refining a TI calculation - additional lambda points
Hannes Loeffler
- [gmx-users] Simulation of nonaqueous solvents
Diana Lousa
- [gmx-users] Simulation of nonaqueous solvents
Diana Lousa
- [gmx-users] cannot find AVX compiler flag
SAKO MIRZAIE
- [gmx-users] metal-surfactant ligand topology
Parthiban Marimuthu
- [gmx-users] fix simulation box corners NVE
Erik Marklund
- [gmx-users] fix simulation box corners NVE
Erik Marklund
- [gmx-users] US perl scripts fails index error
Nikhil Maroli
- [gmx-users] umbrella sampling error
Nikhil Maroli
- [gmx-users] Not enough memory. Failed to calloc :
Nikhil Maroli
- [gmx-users] Not enough memory. Failed to calloc :
Nikhil Maroli
- [gmx-users] reading tpx file (md_0_1.tpr) version 100 with version 83 program:regenerated tpr problem persist
Nikhil Maroli
- [gmx-users] reading tpx file (md_0_1.tpr) version 100 with version 83 program:regenerated tpr problem persist
Nikhil Maroli
- [gmx-users] reading tpx file (md_0_1.tpr) version 100 with version 83 program:regenerated tpr problem persist
Nikhil Maroli
- [gmx-users] Not enough memory. Failed to calloc :
Nikhil Maroli
- [gmx-users] question
Mass
- [gmx-users] question:Justin toturial
Mass
- [gmx-users] HREMD output
Shyno Mathew
- [gmx-users] gmx chi: chi.log output all rotamers always 0
Ebert Maximilian
- [gmx-users] gmx energy block averaging
Andreas Mecklenfeld
- [gmx-users] Error in comparison of Coulomb-14 potential?
Andreas Mecklenfeld
- [gmx-users] pbc
Parvez Mh
- [gmx-users] tabulated dihedral potential
Parvez Mh
- [gmx-users] tabulated dihedral potential
Parvez Mh
- [gmx-users] Installation of two versions of Gromacs on one system
Tushar Ranjan Moharana
- [gmx-users] temperatures of residues
Ali Mohyeddin
- [gmx-users] temperatures of residues
Ali Mohyeddin
- [gmx-users] (no subject)
Sepideh Momeninezhad
- [gmx-users] (no subject)
Sepideh Momeninezhad
- [gmx-users] (no subject)
Sepideh Momeninezhad
- [gmx-users] query on umbrella sampling of association of two plates
Jagannath Mondal
- [gmx-users] Constant Potential on Walls of Electrodes
Alireza Moradzadeh
- [gmx-users] Constant Potential on Walls of Electrodes
Moradzadeh, Alireza
- [gmx-users] Constraints errors
Alireza Moradzadeh
- [gmx-users] Using Lincs
Alireza Moradzadeh
- [gmx-users] Using Lincs
Alireza Moradzadeh
- [gmx-users] Relative alchemical free energy calculations: some confusion about options
Ryan Muraglia
- [gmx-users] Cannot write trajectory frame
Teemu Murtola
- [gmx-users] inserting TM protein dimer into lipid bilayer using Gromacs
Nash, Anthony
- [gmx-users] membed in mdrun VERSION 5.0.4
Nash, Anthony
- [gmx-users] membed in mdrun VERSION 5.0.4
Nash, Anthony
- [gmx-users] membed in mdrun VERSION 5.0.4
Nash, Anthony
- [gmx-users] membed in mdrun VERSION 5.0.4
Nash, Anthony
- [gmx-users] membed in mdrun VERSION 5.0.4
Nash, Anthony
- [gmx-users] Define custom moltype for free energy calculations
Tom Newport
- [gmx-users] distance dependent energy
Cuong Nguyen
- [gmx-users] cut the trajectory in small sub-trajectories
Cuong Nguyen
- [gmx-users] cut the trajectory in small sub-trajectories
Cuong Nguyen
- [gmx-users] cut the trajectory in small sub-trajectories
Cuong Nguyen
- [gmx-users] US perl scripts fails index error
Nikhil
- [gmx-users] question on editconf
Sotirios Dionysios I. Papadatos
- [gmx-users] Normal mode analysis after equilibration
Mario Fernández Pendás
- [gmx-users] Normal mode analysis after equilibration
Mario Fernández Pendás
- [gmx-users] Gromacs Tutorial
XAvier Periole
- [gmx-users] non-bond
Thomas Piggot
- [gmx-users] About Anisotropic NPT equilibration to equilibrate the systm.
Sunil Pokharel
- [gmx-users] Installation of two versions of Gromacs on one system
Szilárd Páll
- [gmx-users] Launch hybrid MPI/openMP run on multiple nodes
Szilárd Páll
- [gmx-users] Launch hybrid MPI/openMP run on multiple nodes
Szilárd Páll
- [gmx-users] Vesicle simulation crashed with dry martini force field
Szilárd Páll
- [gmx-users] Vesicle simulation crashed with dry martini force field
Szilárd Páll
- [gmx-users] multiple nodes, GPUs on a Cray system
Szilárd Páll
- [gmx-users] multiple nodes, GPUs on a Cray system
Szilárd Páll
- [gmx-users] GROMACS performance with an NVidia Tesla k40c
Szilárd Páll
- [gmx-users] Simulation terminated after 260 ns of simulation
Szilárd Páll
- [gmx-users] GROMACS performance with an NVidia Tesla k40c
Szilárd Páll
- [gmx-users] GPU efficiency
Szilárd Páll
- [gmx-users] cannot find AVX compiler flag
Szilárd Páll
- [gmx-users] Restarting Simulations
Soumya Lipsa Rath
- [gmx-users] Restarting Simulations
Soumya Lipsa Rath
- [gmx-users] Gromacs Tutorial
João Rodrigues
- [gmx-users] Constraints in BAR
Dries Van Rompaey
- [gmx-users] pdb2gmx with GROMOS
Dries Van Rompaey
- [gmx-users] pdb2gmx with GROMOS
Dries Van Rompaey
- [gmx-users] Logfile incorrectly (?) has dVbonded/dl terms
Dries Van Rompaey
- [gmx-users] Out of memory error for g_density and trjconv
Wheeler S.R.
- [gmx-users] Implementation of 12-6-4 non-bonded Potential in GROMACS
Biswajit Sadhu
- [gmx-users] find hbond between different groups during simulation
Mahboobe Sadr
- [gmx-users] find hbond between different groups during simulation
Mahboobe Sadr
- [gmx-users] draw histogram
Sana Saeed
- [gmx-users] Serine phosphorylation
Catarina A. Carvalheda dos Santos
- [gmx-users] Serine phosphorylation
Catarina A. Carvalheda dos Santos
- [gmx-users] How to get an index file containing non polar atoms in gromacs?
Catarina A. Carvalheda dos Santos
- [gmx-users] How to get an index file containing non polar atoms in gromacs?
Catarina A. Carvalheda dos Santos
- [gmx-users] Compilation issues with Gromacs 5.1.1 and SGI MPT
Hubert Santuz
- [gmx-users] Compilation issues with Gromacs 5.1.1 and SGI MPT
Hubert Santuz
- [gmx-users] Compilation issues with Gromacs 5.1.1 and SGI MPT
Hubert Santuz
- [gmx-users] Compilation issues with Gromacs 5.1.1 and SGI MPT
Hubert Santuz
- [gmx-users] FFTW with AVX
Oliver Schillinger
- [gmx-users] FFTW with AVX
Oliver Schillinger
- [gmx-users] Problem with DHT residue not found.
Domenico Schitti
- [gmx-users] Problem with DHT residue not found.
Domenico Schitti
- [gmx-users] fix simulation box corners NVE
Sereda, Yuriy Vladimirovich
- [gmx-users] fix simulation box corners NVE
Sereda, Yuriy Vladimirovich
- [gmx-users] Changing a quantity at each time step using a formula
AshutoshAkshay Shah
- [gmx-users] Topology for Sphingomyelin
Ganesh Shahane
- [gmx-users] Topology for Sphingomyelin
Ganesh Shahane
- [gmx-users] Topology for Sphingomyelin
Ganesh Shahane
- [gmx-users] A possible bug in gmx density?
Ganesh Shahane
- [gmx-users] viscosity using green kubo relation for ionic liquids
Shanmuga
- [gmx-users] viscosity using green kubo relation for ionic liquids
Shanmuga
- [gmx-users] Contact_Angles_Calculation
Michael Shirts
- [gmx-users] Contact_Angles_Calculation
Michael Shirts
- [gmx-users] pdb2gmx illegal instruction (core dumped)
Md. Imrul Reza Shishir
- [gmx-users] pdb2gmx illegal instruction (core dumped)
Md. Imrul Reza Shishir
- [gmx-users] pdb2gmx, chain and segment names in the output pdb
Alexey Shvetsov
- [gmx-users] Deuterium order parameter for DPPC
Him Shweta
- [gmx-users] Deuterium order parameter for DPPC
Him Shweta
- [gmx-users] gromacs.org_gmx-users Digest, Vol 141, Issue 115
Him Shweta
- [gmx-users] gromacs.org_gmx-users Digest, Vol 141, Issue 120
Him Shweta
- [gmx-users] genion with Na or Ca
Smith, Micholas D.
- [gmx-users] multiple nodes, GPUs on a Cray system
Smith, Micholas D.
- [gmx-users] multiple nodes, GPUs on a Cray system
Smith, Micholas D.
- [gmx-users] trivial question about water molecules
Smith, Micholas D.
- [gmx-users] protein-protein interaction
Smith, Micholas D.
- [gmx-users] Question
Eric Smoll
- [gmx-users] gmx sasa
Eric Smoll
- [gmx-users] Blender Molecular Visualization Workshop at VizBi 2016
Björn Sommer
- [gmx-users] Simulation of nonaqueous solvents
David van der Spoel
- [gmx-users] hydrophobic interactions
David van der Spoel
- [gmx-users] viscosity using green kubo relation for ionic liquids
David van der Spoel
- [gmx-users] viscosity using green kubo relation for ionic liquids
David van der Spoel
- [gmx-users] Electric field unit
David van der Spoel
- [gmx-users] Electric field unit
David van der Spoel
- [gmx-users] Electric field unit
David van der Spoel
- [gmx-users] Normal mode analysis after equilibration
David van der Spoel
- [gmx-users] Logfile incorrectly (?) has dVbonded/dl terms
David van der Spoel
- [gmx-users] Query on Protein-ligand interaction energy calculation
David van der Spoel
- [gmx-users] pdb2gmx illegal instruction (core dumped)
David van der Spoel
- [gmx-users] Heat capacity (C_{v}) for a solid
David van der Spoel
- [gmx-users] Heat capacity (C_{v}) for a solid
David van der Spoel
- [gmx-users] Error while running gmx_mpi mdrun - Gromacs-5.1.1
Ashalatha Sreshty
- [gmx-users] Water tutorial
Arpita Srivastava
- [gmx-users] Generating topology of 3b68.ent
Peter Stern
- [gmx-users] Serine phosphorylation
Peter Stern
- [gmx-users] Help for gmx enemat
Peter Stern
- [gmx-users] Installation of two versions of Gromacs on one system
Peter Stern
- [gmx-users] Help for gmx enemat
Peter Stern
- [gmx-users] Installation of two versions of Gromacs on one system
Peter Stern
- [gmx-users] Gromacs Tutorial
Peter Stern
- [gmx-users] disabling pbc while using trjconv
Peter Stern
- [gmx-users] How to fix miising atoms in a pdb file?
Seera Suryanarayana
- [gmx-users] Encountered with error after executing the command "gmx solvate"
Seera Suryanarayana
- [gmx-users] Position restraints missing from topol.top
David Swainsbury
- [gmx-users] refining a TI calculation - additional lambda points
Oliwia Maria Szklarczyk
- [gmx-users] Gromos96 53a6 and Berger Lipids
Piggot T.
- [gmx-users] Gromos96 53a6 and Berger Lipids
Piggot T.
- [gmx-users] Build fails with AVX2_256 on Intel Xeon CPU E5-2680 v3
Koji Tanaka
- [gmx-users] Build fails with AVX2_256 on Intel Xeon CPU E5-2680 v3
Koji Tanaka
- [gmx-users] Build fails with AVX2_256 on Intel Xeon CPU E5-2680 v3
Koji Tanaka
- [gmx-users] the end-to-end rotation of a triple helix
Ming Tang
- [gmx-users] GPU efficiency
Stéphane Téletchéa
- [gmx-users] Why GROMACS is generating so many output trajectory files?
Swapnil Wagle
- [gmx-users] split MD trajectory into trajectories of smaller time duration
Swapnil Wagle
- [gmx-users] how to modify the code to generate more controllable checkpoints to restart?
Yong Wang
- [gmx-users] how to modify the code to generate more controllable checkpoints to restart?
Yong Wang
- [gmx-users] how to modify the code to generate more controllable checkpoints to restart?
Yong Wang
- [gmx-users] fix simulation box corners NVE
Tsjerk Wassenaar
- [gmx-users] fix simulation box corners NVE
Tsjerk Wassenaar
- [gmx-users] Correct method to do Cartesian PCA
Tsjerk Wassenaar
- [gmx-users] Correct method to do Cartesian PCA
Tsjerk Wassenaar
- [gmx-users] How to fix miising atoms in a pdb file?
Tsjerk Wassenaar
- [gmx-users] re-weight Metadynamics trajectory from Plumed to make it canonical ensemble
Tsjerk Wassenaar
- [gmx-users] necessary input files during simulation
Tsjerk Wassenaar
- [gmx-users] Constraining positions according to B-factors
Tsjerk Wassenaar
- [gmx-users] Constraining positions according to B-factors
Tsjerk Wassenaar
- [gmx-users] Constraining positions according to B-factors
Tsjerk Wassenaar
- [gmx-users] Problem with DHT residue not found.
Tsjerk Wassenaar
- [gmx-users] cut the trajectory in small sub-trajectories
Tsjerk Wassenaar
- [gmx-users] Query about g_mindist
Tsjerk Wassenaar
- [gmx-users] Position restraints missing from topol.top
Tsjerk Wassenaar
- [gmx-users] Gromacs Tutorial
Tsjerk Wassenaar
- [gmx-users] Gromacs Tutorial
Tsjerk Wassenaar
- [gmx-users] how to modify the code to generate more controllable checkpoints to restart?
Tsjerk Wassenaar
- [gmx-users] the end-to-end rotation of a triple helix
Tsjerk Wassenaar
- [gmx-users] multiple nodes, GPUs on a Cray system
Michael Weiner
- [gmx-users] multiple nodes, GPUs on a Cray system
Michael Weiner
- [gmx-users] g_correlation
Felix W.-H. Weng
- [gmx-users] g_correlation
Felix W.-H. Weng
- [gmx-users] preapration of non-standard residue
Marta Wisniewska
- [gmx-users] doubled atoms
Marta Wisniewska
- [gmx-users] trivial question about water molecules
Marta Wisniewska
- [gmx-users] free energy calculations
Marta Wisniewska
- [gmx-users] Scripts to the gromacs
Elsaid Younes
- [gmx-users] There is no domain decomposition
Ahmet Yıldırım
- [gmx-users] Launch hybrid MPI/openMP run on multiple nodes
Chunlei ZHANG
- [gmx-users] Launch hybrid MPI/openMP run on multiple nodes
Chunlei ZHANG
- [gmx-users] Launch hybrid MPI/openMP run on multiple nodes
Chunlei ZHANG
- [gmx-users] Nvt T-coupling error
Poncho Arvayo Zatarain
- [gmx-users] Tau-t should be at least 20 times larger than nsttcouple*dt
Poncho Arvayo Zatarain
- [gmx-users] Simulation terminated after 260 ns of simulation
anu chandra
- [gmx-users] A question about pressure coupling and random seed generator in microsecond long simulations
anu chandra
- [gmx-users] Simulation runs indefinitely
anu chandra
- [gmx-users] Simulation runs indefinitely
anu chandra
- [gmx-users] How to get an index file containing non polar atoms in gromacs?
Shima ebrahimi
- [gmx-users] non-bonded parameter
m g
- [gmx-users] non-bond
m g
- [gmx-users] Error estimate for order parameter
m g
- [gmx-users] Error bar of order parameter
m g
- [gmx-users] Query about g_mindist
soumadwip ghosh
- [gmx-users] Query about g_mindist
soumadwip ghosh
- [gmx-users] Help for gmx enemat
valerio di giulio
- [gmx-users] Help for gmx enemat
valerio di giulio
- [gmx-users] Help for gmx enemat
valerio di giulio
- [gmx-users] Help for gmx enemat
valerio di giulio
- [gmx-users] Alkane parameters for charm forcefield on gromacs
carlos.navarro87 at gmail.com
- [gmx-users] Alkane parameters for charm forcefield on gromacs
carlos.navarro87 at gmail.com
- [gmx-users] Plumed-2.2.0 installation issue
tarak karmakar
- [gmx-users] AMBER99SB and gaff X OS P X dihedral parameters
tarak karmakar
- [gmx-users] Cannot write trajectory frame
masoud keramati
- [gmx-users] Cannot write trajectory frame
masoud keramati
- [gmx-users] Cannot write trajectory frame
masoud keramati
- [gmx-users] Problem using gromacs
masoud keramati
- [gmx-users] Cannot write trajectory frame
masoud keramati
- [gmx-users] about the output of g_density
ibrahim khalil
- [gmx-users] Problem with editconf
abhishek khetan
- [gmx-users] Simulation of nonaqueous solvents
abhishek khetan
- [gmx-users] Simulation of nonaqueous solvents
abhishek khetan
- [gmx-users] Simulation of nonaqueous solvents
abhishek khetan
- [gmx-users] How to adjust the box size to correct density?
abhishek khetan
- [gmx-users] Simulation of nonaqueous solvents
abhishek khetan
- [gmx-users] Problem in Free Energy Calculations
shagun krishna
- [gmx-users] Problem using gromacs
shagun krishna
- [gmx-users] Problem in Free Energy Calculations
shagun krishna
- [gmx-users] Problem in Free Energy Calculations
shagun krishna
- [gmx-users] Problem in Free Energy Calculations
shagun krishna
- [gmx-users] Regarding value of Elj, Eqq, Clj and Cqq values using LIE Approach
shagun krishna
- [gmx-users] Regarding value of Elj, Eqq, Clj and Cqq values using LIE Approach
shagun krishna
- [gmx-users] Regarding value of Elj, Eqq, Clj and Cqq values using LIE Approach
shagun krishna
- [gmx-users] Regarding value of Elj, Eqq, Clj and Cqq values using LIE Approach
shagun krishna
- [gmx-users] Error while running mdrun with rerun option for LIE calculation
shagun krishna
- [gmx-users] Error while running mdrun with rerun option for LIE calculation
shagun krishna
- [gmx-users] Query on Protein-ligand interaction energy calculation
abhinav kv
- [gmx-users] re-weight Metadynamics trajectory from Plumed to make it canonical ensemble
luigi
- [gmx-users] re-weight Metadynamics trajectory from Plumed to make it canonical ensemble
luigi
- [gmx-users] necessary input files during simulation
mah maz
- [gmx-users] Electric field unit
mah maz
- [gmx-users] necessary input files during simulation
mah maz
- [gmx-users] Electric field unit
mah maz
- [gmx-users] Electric field unit
mah maz
- [gmx-users] Electric field unit
mah maz
- [gmx-users] how to maintain planarity of graphene sheet
jagannath mondal
- [gmx-users] how to maintain planarity of graphene sheet
jagannath mondal
- [gmx-users] how to maintain planarity of graphene sheet
jagannath mondal
- [gmx-users] freeze group in NPT ensemble in gromacs 5.x
jagannath mondal
- [gmx-users] planarity restrain for ligand
ansuman at physics.iisc.ernet.in
- [gmx-users] gromacs.org_gmx-users Digest, Vol 141, Issue 93
lloyd riggs
- [gmx-users] gromacs.org_gmx-users Digest, Vol 141, Issue 93
lloyd riggs
- [gmx-users] gromacs.org_gmx-users Digest, Vol 141, Issue 106
lloyd riggs
- [gmx-users] Temperature Annealing
abdus sabuj
- [gmx-users] Temperature Annealing
abdus sabuj
- [gmx-users] Temperature Annealing
abdus sabuj
- [gmx-users] Temperature Annealing
abdus sabuj
- [gmx-users] Compilation issues with Gromacs 5.1.1 and SGI MPT
hubert santuz
- [gmx-users] how to add martini force field in gromacs
vinshal shalini
- [gmx-users] Problem using gromacs
soumi
- [gmx-users] relative binding free energy calculation Gromacs 5.0.5
hannes.loeffler at stfc.ac.uk
- [gmx-users] Non-Integral Charges
sun
- [gmx-users] Non-Integral Charges
sun
- [gmx-users] Temperature or Pressure Coupling
sun
- [gmx-users] Temperature or Pressure Coupling
sun
- [gmx-users] ionic liquids - viscosity using green kubo relation
shanmuga sundaram
- [gmx-users] viscosity using green kubo relation for ionic liquids
shanmuga sundaram
- [gmx-users] viscosity using green kubo relation for ionic liquids
shanmuga sundaram
- [gmx-users] High temperature simulation with GROMOS96 54a7
sunita at tifrh.res.in
- [gmx-users] gromacs.org_gmx-users Digest, Vol 141, Issue 121
sunita at tifrh.res.in
- [gmx-users] g-membed +KALP in dppc
neda razavi
- [gmx-users] MSD calculation
凌未风
- [gmx-users] Problem in using pdb2gmx to generate top file
张敏华
Last message date:
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Archived on: Sun Jan 31 20:36:12 CET 2016
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