August 2017 Archives by date

Messages sorted by: [ thread ] [ subject ] [ author ]
More info on this list...

Starting: Tue Aug 1 00:11:02 CEST 2017
Ending: Thu Aug 31 22:38:58 CEST 2017
Messages: 643

[gmx-users] hole in the simulation box Dallas Warren
[gmx-users] gmx mdmat calculation of heavy atoms of two side chains Justin Lemkul
[gmx-users] Creating Custom .rtp files Justin Lemkul
[gmx-users] gromacs rerun calculate the energy Justin Lemkul
[gmx-users] How can I implement a radial potential field in GROMACS? Justin Lemkul
[gmx-users] ligand topology Justin Lemkul
[gmx-users] Question on Umbrella Sampling with varied ionic strength. Justin Lemkul
[gmx-users] Question on Umbrella Sampling with varied ionic strength. Yuanchao Liu (MSU)
[gmx-users] ligand topology Mohammad Zahidul Hossain Khan
[gmx-users] Reg. Umbrella sampling problem with direction "가디 장데부 고라크스나트"
[gmx-users] gromacs.org_gmx-users Digest, Vol 160, Issue 1 Мижээ Батсайхан
[gmx-users] Some problem about the process of calculating MM-PBSA binding free energy yujie Liu
[gmx-users] gromacs.org_gmx-users Digest, Vol 160, Issue 2 王珍
[gmx-users] Some problem about the process of calculating MM-PBSA binding free energy David van der Spoel
[gmx-users] (no subject) yujie Liu
[gmx-users] Some problem about the process of calculating MM-PBSA binding free energy 刘玉杰
[gmx-users] Can not write a pdb file without atom names (concatenating 2 pdb files) Andrew Bostick
[gmx-users] PCA in dihdral space Gleb Novikov
[gmx-users] Estimation of the rotations during CG simulations Gleb Novikov
[gmx-users] Alchemical transformation position restrains for B state and citing literature for H-RETI Hermann, Johannes
[gmx-users] pme algorithm 王珍
[gmx-users] ligand topology Suhaib Shekfeh
[gmx-users] pulling of a molecule through protein-membrane system Alex Mathew
[gmx-users] Creating Custom .rtp files Momin Ahmad
[gmx-users] LINCS warning during energy minimization of nitrogen with virtual site Ali Ahmed
[gmx-users] ligand topology Alan
[gmx-users] LINCS warning during energy minimization of nitrogen with virtual site Mark Abraham
[gmx-users] ligand topology Mohammad Zahidul Hossain Khan
[gmx-users] LINCS warning during energy minimization of nitrogen with virtual site Ali Ahmed
[gmx-users] ligand topology Lucio Ricardo Montero Valenzuela
[gmx-users] ligand topology Justin Lemkul
[gmx-users] Creating Custom .rtp files Justin Lemkul
[gmx-users] pulling of a molecule through protein-membrane system Justin Lemkul
[gmx-users] Doubt about hessian matrix in Normal mode analysis Varvdekar Bhagyesh Rajendra
[gmx-users] Umbrella Sampling with Direction-Periodic Daniel Kozuch
[gmx-users] Doubt about hessian matrix in Normal mode analysis Varvdekar Bhagyesh Rajendra
[gmx-users] gromacs rerun calculate the energy Varvdekar Bhagyesh Rajendra
[gmx-users] Doubt about hessian matrix in Normal mode analysis Varvdekar Bhagyesh Rajendra
[gmx-users] gromacs rerun calculate the energy Mark Abraham
[gmx-users] ligand topology Mohammad Zahidul Hossain Khan
[gmx-users] LINCS warning during energy minimization of nitrogen with virtual site Dallas Warren
[gmx-users] ligand topology Alan
[gmx-users] ligand topology Mark Abraham
[gmx-users] LINCS warning during energy minimization of nitrogen with virtual site Ali Ahmed
[gmx-users] LINCS warning during energy minimization of nitrogen with virtual site Justin Lemkul
[gmx-users] ligand topology Mohammad Zahidul Hossain Khan
[gmx-users] Reg. Umbrella sampling problem with direction "가디 장데부 고라크스나트"
[gmx-users] pulling of a molecule through protein-membrane system Alex Mathew
[gmx-users] GPU job failed Albert
[gmx-users] membrane-protein simulation Amir Zeb
[gmx-users] Creating Custom .rtp files Momin Ahmad
[gmx-users] Clayff forcefield G R
[gmx-users] -multidir option in REMD (GROMACS v2016.1) ABEL Stephane
[gmx-users] -multidir option in REMD (GROMACS v2016.1) Hermann, Johannes
[gmx-users] -multidir option in REMD (GROMACS v2016.1) Mark Abraham
[gmx-users] GPU job failed Mark Abraham
[gmx-users] Error in the replica order in REMD (GMX v2016.1) ABEL Stephane
[gmx-users] Error in the replica order in REMD (GMX v2016.1) Mark Abraham
[gmx-users] Error in the replica order in REMD (GMX v2016.1) Mark Abraham
[gmx-users] Error in the replica order in REMD (GMX v2016.1) Hermann, Johannes
[gmx-users] hole in the simulation box edesantis
[gmx-users] GPU job failed Albert
[gmx-users] QM/MM in Gromacs-5.1.4? Albert
[gmx-users] Dynamics only for cavity in molecule. nikolaev at spbau.ru
[gmx-users] LINCS warning during energy minimization of nitrogen with virtual site Ali Ahmed
[gmx-users] Fwd: meaning of -sigfac option in gmx sigeps Tamisra Pal
[gmx-users] Error in itp file Souvik Dey
[gmx-users] Error in itp file Mohammad Zahidul Hossain Khan
[gmx-users] Creating Custom .rtp files Justin Lemkul
[gmx-users] membrane-protein simulation Justin Lemkul
[gmx-users] pulling of a molecule through protein-membrane system Justin Lemkul
[gmx-users] Error in itp file Justin Lemkul
[gmx-users] LINCS warning during energy minimization of nitrogen with virtual site Justin Lemkul
[gmx-users] Clayff forcefield Justin Lemkul
[gmx-users] -multidir option in REMD (GROMACS v2016.1) -resolved ABEL Stephane
[gmx-users] QM/MM in Gromacs-5.1.4? Clinton King
[gmx-users] G_MMPBSA Suhaib Shekfeh
[gmx-users] CHARMM36 for GMX Alex
[gmx-users] CHARMM36 for GMX Justin Lemkul
[gmx-users] CHARMM36 for GMX Alex
[gmx-users] CHARMM36 for GMX Justin Lemkul
[gmx-users] CHARMM36 for GMX Alex
[gmx-users] CHARMM36 for GMX Justin Lemkul
[gmx-users] segmentation fault for unknown reason gangotri dey
[gmx-users] CHARMM36 for GMX Alex
[gmx-users] AVX related compiler error during build with P100 RHEL7 Guyen Gn
[gmx-users] AVX related compiler error during build with P100 RHEL7 Mark Abraham
[gmx-users] membrane-protein simulation Amir Zeb
[gmx-users] x2top and default dihedral type Alex
[gmx-users] Can not write a pdb file without atom names (concatenating 2 pdb files) Andrew Bostick
[gmx-users] Alchemical transformation position restrains for B state and citing literature for H-RETI Hermann, Johannes
[gmx-users] Can not write a pdb file without atom names (concatenating 2 pdb files) Mark Abraham
[gmx-users] Protein coming out of simulation box. zaved at tezu.ernet.in
[gmx-users] Can not write a pdb file without atom names (concatenating 2 pdb files) Andrew Bostick
[gmx-users] Clustering Pandya, Akash
[gmx-users] Can not write a pdb file without atom names (concatenating 2 pdb files) Mark Abraham
[gmx-users] Protein coming out of simulation box. Mark Abraham
[gmx-users] Protein coming out of simulation box. Mark Abraham
[gmx-users] evaluation of simulated frames by procheck Seera Suryanarayana
[gmx-users] Error in itp file Souvik Dey
[gmx-users] Error in itp file Souvik Dey
[gmx-users] meaning of -sigfac option in gmx sigeps Tamisra Pal
[gmx-users] mutagenesis- Study the role of an aminoacids in proteins. Nikhil Maroli
[gmx-users] meaning of -sigfac option in gmx sigeps Mark Abraham
[gmx-users] Pulling Luca Retattino
[gmx-users] Gromacs 2016 pulling code Luca Retattino
[gmx-users] Error in itp file Mohammad Zahidul Hossain Khan
[gmx-users] Problems with continuing simulation after time limit Searle Duay
[gmx-users] Problems with continuing simulation after time limit Mark Abraham
[gmx-users] Error in itp file Mohammad Zahidul Hossain Khan
[gmx-users] segmentation fault for unknown reason Justin Lemkul
[gmx-users] Error in itp file Justin Lemkul
[gmx-users] Does gmx distance correct for broken molecules from pbc? Ramon Crehuet
[gmx-users] Does gmx distance correct for broken molecules from pbc? Mark Abraham
[gmx-users] The small organic molecule occurred deformation during simulation yujie liu
[gmx-users] Could not find clayff forcefield G R
[gmx-users] Error in itp file Souvik Dey
[gmx-users] Problem with dihedral restraints gangotri dey
[gmx-users] question about gmx do_dssp YanhuaOuyang
[gmx-users] Problem with dihedral restraints Mark Abraham
[gmx-users] question about gmx do_dssp Mark Abraham
[gmx-users] Problem with dihedral restraints gangotri dey
[gmx-users] Gmx hbond farial tavakoli
[gmx-users] MnO2 periodic system gangotri dey
[gmx-users] Dynamics only for cavity in molecule. nikolaev at spbau.ru
[gmx-users] Dynamics only for cavity in molecule. Mark Abraham
[gmx-users] error at nvt equilibrium Mohammad Zahidul Hossain Khan
[gmx-users] Dynamics only for cavity in molecule. nikolaev at spbau.ru
[gmx-users] Dynamics only for cavity in molecule. Mark Abraham
[gmx-users] Help with segmentation fault error Kunal Maniar
[gmx-users] question about gmx do_dssp YanhuaOuyang
[gmx-users] Generating topology file for a long polymer chain Mahsa E
[gmx-users] Generating topology file for a long polymer chain Mahsa E
[gmx-users] QSUB commands Neha Gupta
[gmx-users] Umbrella Sampling -PME mohamed mehana
[gmx-users] question about gmx do_dssp Mark Abraham
[gmx-users] QSUB commands Mark Abraham
[gmx-users] question about gmx do_dssp Justin Lemkul
[gmx-users] Generating topology file for a long polymer chain Justin Lemkul
[gmx-users] Gmx hbond Justin Lemkul
[gmx-users] Could not find clayff forcefield Justin Lemkul
[gmx-users] The small organic molecule occurred deformation during simulation Justin Lemkul
[gmx-users] The small organic molecule occurred deformation during simulation yujie liu
[gmx-users] The small organic molecule occurred deformation during simulation yujie liu
[gmx-users] Continuing a run ‪Mohammad Roostaie‬ ‪
[gmx-users] TOPOLOGY USING OPLS FORCEFIELD Vidya R
[gmx-users] TOPOLOGY USING OPLS FORCEFIELD Nikhil Maroli
[gmx-users] How to Identify clusters Sameer Edirisinghe
[gmx-users] Non bonded interaction mapping Sameer Edirisinghe
[gmx-users] How to Identify clusters Anna Lappala
[gmx-users] How to Identify clusters Anna Lappala
[gmx-users] How to obtain a proper structure for glycine? ZHANG Cheng
[gmx-users] How to obtain a proper structure for glycine? Mark Abraham
[gmx-users] How to obtain a proper structure for glycine? Mark Abraham
[gmx-users] How to obtain a proper structure for glycine? ZHANG Cheng
[gmx-users] How to obtain a proper structure for glycine? ZHANG Cheng
[gmx-users] How to obtain a proper structure for glycine? Dawid das
[gmx-users] How to obtain a proper structure for glycine? ZHANG Cheng
[gmx-users] How to obtain a proper structure for glycine? ZHANG Cheng
[gmx-users] How to obtain a proper structure for glycine? Dawid das
[gmx-users] Gmx hbond farial tavakoli
[gmx-users] Constraining starting configuration in Coarse-Grain Simulation Maghesree Chakraborty
[gmx-users] Generating topology file for a long polymer chain Mahsa E
[gmx-users] trans-membrane protein simulation Amir Zeb
[gmx-users] time calculations faru honey
[gmx-users] converting xtc to pdb without need to tpr file using trjconv Neda Rafiee
[gmx-users] amino acid adsorption on metal surface Rabia Mukhtar
[gmx-users] Could not find clayff forcefield G R
[gmx-users] 2D maps Yasser Almeida Hernández
[gmx-users] Visualization of xtc file farial tavakoli
[gmx-users] Visualization of xtc file Andrea Spitaleri
[gmx-users] Visualization of xtc file farial tavakoli
[gmx-users] How to configure the gro/itp/top files after running "insert-molecules"? ZHANG Cheng
[gmx-users] -com and -rdf options do not work in gmx rdf analysis faride badalkhani
[gmx-users] How to configure the gro/itp/top files after running "insert-molecules"? yujie liu
[gmx-users] Performance values Szilárd Páll
[gmx-users] Performance values Szilárd Páll
[gmx-users] Non Standard residues moving Away Souvik Dey
[gmx-users] How to configure the gro/itp/top files after running "insert-molecules"? Souvik Dey
[gmx-users] The small organic molecule occurred deformation during simulation Justin Lemkul
[gmx-users] Gmx hbond Justin Lemkul
[gmx-users] (no subject) gangotri dey
[gmx-users] Generating topology file for a long polymer chain Justin Lemkul
[gmx-users] trans-membrane protein simulation Justin Lemkul
[gmx-users] converting xtc to pdb without need to tpr file using trjconv Justin Lemkul
[gmx-users] How to configure the gro/itp/top files after running "insert-molecules"? ZHANG Cheng
[gmx-users] Performance values Maureen Chew
[gmx-users] converting xtc to pdb without need to tpr file using trjconv Neda Rafiee
[gmx-users] Non Standard residues moving Away Mark Abraham
[gmx-users] How to Identify clusters Mark Abraham
[gmx-users] Constraining starting configuration in Coarse-Grain Simulation Mark Abraham
[gmx-users] Non Standard residues moving Away Souvik Dey
[gmx-users] Non Standard residues moving Away Justin Lemkul
[gmx-users] Constraining starting configuration in Coarse-Grain Simulation Maghesree Chakraborty
[gmx-users] solvate only in the z-direction gangotri dey
[gmx-users] clayff forcefield G R
[gmx-users] Constraining starting configuration in Coarse-Grain Simulation Mark Abraham
[gmx-users] clayff forcefield Mark Abraham
[gmx-users] solvate only in the z-direction Mark Abraham
[gmx-users] (no subject) Mark Abraham
[gmx-users] time calculations Mark Abraham
[gmx-users] (no subject) gangotri dey
[gmx-users] Memory issues using -ac option of gmx hbond Jared Sagendorf
[gmx-users] Memory issues using -ac option of gmx hbond Smith, Micholas D.
[gmx-users] (no subject) Mark Abraham
[gmx-users] Memory issues using -ac option of gmx hbond Mark Abraham
[gmx-users] (no subject) Alex
[gmx-users] [gmx-developers] importing amber parameters to gromacs format? Justin Lemkul
[gmx-users] MnO2 periodic system Dallas Warren
[gmx-users] clayff forcefield G R
[gmx-users] clayff forcefield Justin Lemkul
[gmx-users] (no subject) Sorour Hasani
[gmx-users] Generating topology file for a long polymer chain Mahsa E
[gmx-users] convert .tpr to include energy groups Tushar Ranjan Moharana
[gmx-users] Problem with Ryzen, threads and core dumps? Steffen Graether
[gmx-users] vdw and Electrostatic energy Mohammad Zahidul Hossain Khan
[gmx-users] (no subject) Justin Lemkul
[gmx-users] convert .tpr to include energy groups Justin Lemkul
[gmx-users] vdw and Electrostatic energy Justin Lemkul
[gmx-users] MM/PBSA Kingsley Theras Primus Dass .
[gmx-users] MM/PBSA Amir Zeb
[gmx-users] GETTING GOOD PERFORMANCE FROM MDRUN Vidya R
[gmx-users] MM/PBSA Kingsley Theras Primus Dass .
[gmx-users] GETTING GOOD PERFORMANCE FROM MDRUN Nikhil Maroli
[gmx-users] MM/PBSA Amir Zeb
[gmx-users] Ris: MM/PBSA Andrea Spitaleri
[gmx-users] convert .tpr to include energy groups Tushar Ranjan Moharana
[gmx-users] clayff forcefield G R
[gmx-users] clayff forcefield Mark Abraham
[gmx-users] clayff forcefield Mark Abraham
[gmx-users] Position restrains during alchemical transformation Hermann, Johannes
[gmx-users] Position restrains during alchemical transformation Mark Abraham
[gmx-users] Position restrains during alchemical transformation Mark Abraham
[gmx-users] Atom OXT in residue was not found Qinghua Liao
[gmx-users] Atom OXT in residue was not found Justin Lemkul
[gmx-users] g_hbonds calculation on GPU Rituraj Purohit
[gmx-users] remove the jumps over the boundaries ‪farial tavakoli‬ ‪
[gmx-users] g_hbonds calculation on GPU Erik Marklund
[gmx-users] Problem with Ryzen, threads and core dumps? Mark Abraham
[gmx-users] Atom OXT in residue was not found Qinghua Liao
[gmx-users] electronic fields Li, Tong
[gmx-users] g_cluster and g_hbond calculation on GPU Kishwar Hayat Khan
[gmx-users] remove the jumps over the boundaries Milan Melichercik
[gmx-users] g_cluster and g_hbond calculation on GPU Mark Abraham
[gmx-users] remove the jumps over the boundaries farial tavakoli
[gmx-users] Constraining starting configuration in Coarse-Grain Simulation Maghesree Chakraborty
[gmx-users] transmembrane protein simulation abhisek Mondal
[gmx-users] (no subject) gangotri dey
[gmx-users] (no subject) Alex
[gmx-users] transmembrane protein simulation Justin Lemkul
[gmx-users] gmx sasa Mohammad Zahidul Hossain Khan
[gmx-users] (no subject) saranya
[gmx-users] (no subject) saranya
[gmx-users] (no subject) Tasneem Kausar
[gmx-users] problem with n2t file Niko Ukkonen
[gmx-users] grompp warning Qinghua Liao
[gmx-users] (no subject) Iman Ahmadabadi
[gmx-users] Position restrains during alchemical transformation Hermann, Johannes
[gmx-users] problem with n2t file Justin Lemkul
[gmx-users] gmx sasa Justin Lemkul
[gmx-users] Potential Shift Verlet Natalie Paige Schieber
[gmx-users] Donors and Acceptors - gmx hbond Marcelo Depólo
[gmx-users] (no subject) saranya
[gmx-users] non zero free energy values in mass transformation deepak bapat
[gmx-users] non zero free energy values in mass transformation André Farias de Moura
[gmx-users] non zero free energy values in mass transformation Dan Gil
[gmx-users] (no subject) Dan Gil
[gmx-users] Non bonded interaction mapping Dan Gil
[gmx-users] Simulations showing that mass contributes to the solvation free energy in a thermodynamic cycle Dan Gil
[gmx-users] Pull Code: direction-periodic with 3 dimensions Daniel Kozuch
[gmx-users] Pull Code: direction-periodic with 3 dimensions Justin Lemkul
[gmx-users] Pull Code: direction-periodic with 3 dimensions Daniel Kozuch
[gmx-users] Recent successful compile on Mac Pro with OpenCL? Failing Test #20: MdrunTests Steffen Graether
[gmx-users] non zero free energy values in mass transformation deepak bapat
[gmx-users] ligand ‪farial tavakoli‬ ‪
[gmx-users] Magic Number Error in XTC file (read 0, should be 1995) ZHANG Cheng
[gmx-users] Magic Number Error in XTC file (read 0, should be 1995) ZHANG Cheng
[gmx-users] Magic Number Error in XTC file (read 0, should be 1995) Justin Lemkul
[gmx-users] ligand Justin Lemkul
[gmx-users] Magic Number Error in XTC file (read 0, should be 1995) ZHANG Cheng
[gmx-users] Magic Number Error in XTC file (read 0, should be 1995) Justin Lemkul
[gmx-users] Magic Number Error in XTC file (read 0, should be 1995) ZHANG Cheng
[gmx-users] NVT error Justin Lemkul
[gmx-users] Magic Number Error in XTC file (read 0, should be 1995) Justin Lemkul
[gmx-users] ligand farial tavakoli
[gmx-users] ligand Justin Lemkul
[gmx-users] Difference in omega angles!! Seera Suryanarayana
[gmx-users] Difference in omega angles!! Justin Lemkul
[gmx-users] Difference in omega angles!! Alex
[gmx-users] Difference in omega angles!! Justin Lemkul
[gmx-users] non zero free energy values in mass transformation deepak bapat
[gmx-users] ligand ‪farial tavakoli‬ ‪
[gmx-users] PBC ISSUES IN GROMACS Neha Gupta
[gmx-users] PBC ISSUES IN GROMACS David van der Spoel
[gmx-users] Drift with groups+tabulated potential. sperez14 at us.es
[gmx-users] Position Restraint for production MD Pandya, Akash
[gmx-users] Position Restraint for production MD Justin Lemkul
[gmx-users] ligand Justin Lemkul
[gmx-users] Position Restraint for production MD Mark Abraham
[gmx-users] PBC ISSUES IN GROMACS Mark Abraham
[gmx-users] Recent successful compile on Mac Pro with OpenCL? Failing Test #20: MdrunTests Mark Abraham
[gmx-users] Recent successful compile on Mac Pro with OpenCL? Failing Test #20: MdrunTests Mark Abraham
[gmx-users] Donors and Acceptors - gmx hbond Mark Abraham
[gmx-users] Donors and Acceptors - gmx hbond Mark Abraham
[gmx-users] Potential Shift Verlet Mark Abraham
[gmx-users] Can I specify the residue numbers for RMSD? ZHANG Cheng
[gmx-users] Can I specify the residue numbers for RMSD? Justin Lemkul
[gmx-users] Recent successful compile on Mac Pro with OpenCL? Failing Test #20: MdrunTests Steffen Graether
[gmx-users] Problem with Ryzen, threads and core dumps? Steffen Graether
[gmx-users] ligand farial tavakoli
[gmx-users] gromacs.org_gmx-users Digest, Vol 160, Issue 63 Faez Iqbal Khan
[gmx-users] gromacs.org_gmx-users Digest, Vol 160, Issue 63 Faez Iqbal Khan
[gmx-users] Donors and Acceptors - gmx hbond - gromacs.org_gmx-users Digest, Vol 160, Issue 67 Marcelo Depólo
[gmx-users] NVT error Justin Lemkul
[gmx-users] Recent successful compile on Mac Pro with OpenCL? Failing Test #20: MdrunTests Mark Abraham
[gmx-users] How to use the index.ndx when running rms? ZHANG Cheng
[gmx-users] How to use the index.ndx when running rms? Justin Lemkul
[gmx-users] non zero free energy values in mass transformation Dan Gil
[gmx-users] How to use the index.ndx when running rms? ZHANG Cheng
[gmx-users] Recent successful compile on Mac Pro with OpenCL? Failing Test #20: MdrunTests Steffen Graether
[gmx-users] How to use the index.ndx when running rms? ZHANG Cheng
[gmx-users] Question on gmx_wham with two reaction coordinates. Yuanchao Liu (MSU)
[gmx-users] Kudos to trjconv -pbc cluster coder Dallas Warren
[gmx-users] umbrella sampling Kingsley Theras Primus Dass .
[gmx-users] Scaling in gromacs praveen kumar
[gmx-users] ligand ‪farial tavakoli‬ ‪
[gmx-users] Fwd: saranya
[gmx-users] Fwd: Justin Lemkul
[gmx-users] (Don't know if mail worked last time)Drift with groups+tabulated potential. sperez14 at us.es
[gmx-users] how to make molecular model with both ion channel and lipid bilayer? Li, Tong
[gmx-users] how to make molecular model with both ion channel and lipid bilayer? h.alizadeh at znu.ac.ir
[gmx-users] Doing restart ‪farial tavakoli‬ ‪
[gmx-users] npt simulation error Mohammad Zahidul Hossain Khan
[gmx-users] npt simulation error Justin Lemkul
[gmx-users] npt simulation error Mohammad Zahidul Hossain Khan
[gmx-users] positioning molecule at desired location Alex Mathew
[gmx-users] (no subject) zaved at tezu.ernet.in
[gmx-users] (no subject) RAHUL SURESH
[gmx-users] Fwd: saranya
[gmx-users] gromacs.org_gmx-users Digest, Vol 160, Issue 74 Naba
[gmx-users] COM pulling Naba
[gmx-users] non zero free energy values in mass transformation deepak bapat
[gmx-users] Compiling DSSP-2.2.1 from source João Henriques
[gmx-users] gromacs.org_gmx-users Digest, Vol 160, Issue 75 zaved at tezu.ernet.in
[gmx-users] Compiling DSSP-2.2.1 from source João Henriques
[gmx-users] Recent successful compile on Mac Pro with OpenCL? Failing Test #20: MdrunTests Steffen Graether
[gmx-users] Regarding naming dipeptide in charmm36 Forcefield Dilip H N
[gmx-users] npt simulation error Justin Lemkul
[gmx-users] positioning molecule at desired location Justin Lemkul
[gmx-users] Fwd: Justin Lemkul
[gmx-users] COM pulling Justin Lemkul
[gmx-users] Regarding naming dipeptide in charmm36 Forcefield Justin Lemkul
[gmx-users] Gromacs enquiry Odame Agyapong
[gmx-users] npt simulation error Mohammad Zahidul Hossain Khan
[gmx-users] Recent successful compile on Mac Pro with OpenCL? Failing Test #20: MdrunTests Mark Abraham
[gmx-users] Scaling in gromacs Mark Abraham
[gmx-users] Pbc farial tavakoli
[gmx-users] dielectric constant 4 Mohammad Zahidul Hossain Khan
[gmx-users] InflateGRO script "가디 장데부 고라크스나트"
[gmx-users] dielectric constant 4 Alex
[gmx-users] Regarding naming dipeptide in charmm36 Forcefield Dilip H N
[gmx-users] dielectric constant 4 Mohammad Zahidul Hossain Khan
[gmx-users] InflateGRO script Odame Agyapong
[gmx-users] Gromacs enquiry Mark Abraham
[gmx-users] dielectric constant 4 Mark Abraham
[gmx-users] Gromacs enquiry Odame Agyapong
[gmx-users] surfactants simulation topology generation with Automated Topology Builder and lincs warnings edesantis
[gmx-users] Gromacs enquiry Mark Abraham
[gmx-users] Gromacs enquiry Subhomoi Borkotoky
[gmx-users] surfactants simulation topology generation with Automated Topology Builder and lincs warnings Peter Kroon
[gmx-users] Software inconsistency error: Lost particles while sorting Alex Mathew
[gmx-users] Pbc Justin Lemkul
[gmx-users] Regarding naming dipeptide in charmm36 Forcefield Justin Lemkul
[gmx-users] InflateGRO script Justin Lemkul
[gmx-users] dielectric constant 4 Mohammad Zahidul Hossain Khan
[gmx-users] dielectric constant 4 Justin Lemkul
[gmx-users] Use of providing -ix pullx.xvg in WHAM jay patil
[gmx-users] extending umbrella sampling simulations Irem Altan
[gmx-users] CHARMM36 & Gromacs Mateusz Marianski
[gmx-users] surfactants simulation topology generation with Automated Topology Builder and lincs warnings Piggot T.
[gmx-users] periodic boundary conditions JAVAD MAHMOUDZADEH
[gmx-users] Dear gmx-users, Sithara Perera
[gmx-users] Applying a potential gradient Sithara Perera
[gmx-users] ForceField of ethanol and the default parameters in Gromacs ZUO Taisen
[gmx-users] Regarding naming dipeptide in charmm36 Forcefield Dilip H N
[gmx-users] RDF RAHUL SURESH
[gmx-users] problem in extending a simulation run manindersingh rajawat
[gmx-users] How to convert C6&C12 from GROMOS54a7 to sigma&epsilon for OPLSAA Ming Tang
[gmx-users] surfactants simulation topology generation with Automated Topology Builder and lincs warnings Peter Kroon
[gmx-users] problem in extending a simulation run Tasneem Kausar
[gmx-users] Error with MPICH Souparno Adhikary
[gmx-users] problem in extending a simulation run manindersingh rajawat
[gmx-users] RDF Dan Gil
[gmx-users] RDF RAHUL SURESH
[gmx-users] surfactants simulation topology generation with Automated Topology Builder and lincs warnings Thomas Piggot
[gmx-users] Error with MPICH Mark Abraham
[gmx-users] ForceField of ethanol and the default parameters in Gromacs Mark Abraham
[gmx-users] ForceField of ethanol and the default parameters in Gromacs Mark Abraham
[gmx-users] Error with MPICH Souparno Adhikary
[gmx-users] Software inconsistency error: Lost particles while sorting Mark Abraham
[gmx-users] problem in extending a simulation run Mark Abraham
[gmx-users] surfactants simulation topology generation with Automated Topology Builder and lincs warnings edesantis
[gmx-users] RDF Dan Gil
[gmx-users] surfactants simulation topology generation with Automated Topology Builder and lincs warnings Thomas Piggot
[gmx-users] umbrella sample Question yujie liu
[gmx-users] surfactants simulation topology generation with Automated Topology Builder and lincs warnings Thomas Piggot
[gmx-users] surfactants simulation topology generation with Automated Topology Builder and lincs warnings edesantis
[gmx-users] surfactants simulation topology generation with Automated Topology Builder and lincs warnings Thomas Piggot
[gmx-users] surfactants simulation topology generation with Automated Topology Builder and lincs warnings Thomas Piggot
[gmx-users] Use of providing -ix pullx.xvg in WHAM Justin Lemkul
[gmx-users] CHARMM36 & Gromacs Justin Lemkul
[gmx-users] Regarding naming dipeptide in charmm36 Forcefield Justin Lemkul
[gmx-users] How to convert C6&C12 from GROMOS54a7 to sigma&epsilon for OPLSAA Justin Lemkul
[gmx-users] umbrella sample Question Justin Lemkul
[gmx-users] How to convert C6&C12 from GROMOS54a7 to sigma&epsilon for OPLSAA Ming Tang
[gmx-users] How to convert C6&C12 from GROMOS54a7 to sigma&epsilon for OPLSAA Justin Lemkul
[gmx-users] umbrella sample Question yujie liu
[gmx-users] setting up simulated annealing Seera Suryanarayana
[gmx-users] Simulated annealing Seera Suryanarayana
[gmx-users] surfactants simulation topology generation with Automated Topology Builder and lincs warnings edesantis
[gmx-users] umbrella sample Question Nikhil Maroli
[gmx-users] Pressure coupling incorrect number of values (I need exactly 2)-US simulation Alex Mathew
[gmx-users] problem in extending a simulation run manindersingh rajawat
[gmx-users] Use of providing -ix pullx.xvg in WHAM jay patil
[gmx-users] Question about the No chi1 & chi2 angle problem with gmx Chi Xingcheng Lin
[gmx-users] umbrella sample Question Justin Lemkul
[gmx-users] Pressure coupling incorrect number of values (I need exactly 2)-US simulation Justin Lemkul
[gmx-users] Question about the No chi1 & chi2 angle problem with gmx Chi Justin Lemkul
[gmx-users] HSE in Charmm-gui membrane builder Мижээ Батсайхан
[gmx-users] Pressure coupling incorrect number of values (I need exactly 2)-US simulation Alex Mathew
[gmx-users] Pressure coupling incorrect number of values (I need exactly 2)-US simulation Alex
[gmx-users] umbrella sample Question yujie liu
[gmx-users] HSE in Charmm-gui membrane builder Nikhil Maroli
[gmx-users] HSE in Charmm-gui membrane builder Justin Lemkul
[gmx-users] Average and bfactors.pdb farial tavakoli
[gmx-users] Calculating the dielectric constant of a ligand Sajad Ahrari
[gmx-users] Regarding naming dipeptide in charmm36 Forcefield Dilip H N
[gmx-users] Regarding naming dipeptide in charmm36 Forcefield Justin Lemkul
[gmx-users] Average and bfactors.pdb Justin Lemkul
[gmx-users] Doubt about hessian matrix in Normal mode analysis Varvdekar Bhagyesh Rajendra
[gmx-users] Average and bfactors.pdb farial tavakoli
[gmx-users] Setting up SA Seera Suryanarayana
[gmx-users] Setting up SA Nikhil Maroli
[gmx-users] How to convert C6&C12 from GROMOS54a7 to sigma&epsilon for OPLSAA Ming Tang
[gmx-users] Pressure coupling incorrect number of values (I need exactly 2)-US simulation Alex Mathew
[gmx-users] Error in simulated annealing Seera Suryanarayana
[gmx-users] Residue 1 mapping problem? morpheus
[gmx-users] MPICH2 error Souparno Adhikary
[gmx-users] MPICH2 error Mark Abraham
[gmx-users] FEP calculations on multiple nodes Vikas Dubey
[gmx-users] MPICH2 error Souparno Adhikary
[gmx-users] MPICH2 error Mark Abraham
[gmx-users] MPICH2 error Souparno Adhikary
[gmx-users] Fwd: Question on gmx_wham with two reaction coordinates. Yuanchao Liu (MSU)
[gmx-users] Average and bfactors.pdb Justin Lemkul
[gmx-users] Error in simulated annealing Justin Lemkul
[gmx-users] Residue 1 mapping problem? Justin Lemkul
[gmx-users] FEP calculations on multiple nodes Michael Shirts
[gmx-users] FEP calculations on multiple nodes Vikas Dubey
[gmx-users] Regarding Unknown cmap torsion between atoms Dilip H N
[gmx-users] Regarding Unknown cmap torsion between atoms Mark Abraham
[gmx-users] FEP calculations on multiple nodes Nikhil Maroli
[gmx-users] Regarding Unknown cmap torsion between atoms Dilip H N
[gmx-users] Regarding Unknown cmap torsion between atoms Mark Abraham
[gmx-users] Trouble with gmx distance Sotirios Dionysios I. Papadatos
[gmx-users] FEP calculations on multiple nodes Vikas Dubey
[gmx-users] Average and bfactors.pdb farial tavakoli
[gmx-users] FEP calculations on multiple nodes Nikhil Maroli
[gmx-users] Regarding Unknown cmap torsion between atoms Dilip H N
[gmx-users] Fwd: Unusual bonding between residues in vmd ISHRAT JAHAN
[gmx-users] Regarding Unknown cmap torsion between atoms Mark Abraham
[gmx-users] Fwd: Unusual bonding between residues in vmd Mark Abraham
[gmx-users] Fwd: Unusual bonding between residues in vmd Mark Abraham
[gmx-users] Regarding Unknown cmap torsion between atoms Dilip H N
[gmx-users] Fwd: Unusual bonding between residues in vmd ISHRAT JAHAN
[gmx-users] Fwd: Unusual bonding between residues in vmd ISHRAT JAHAN
[gmx-users] Fwd: Unusual bonding between residues in vmd Nikhil Maroli
[gmx-users] COM pulling with gromacs 5.0.x Romain Gautier IPMC
[gmx-users] Gromacs_GPU_Compiling_Problem 郭逸峰
[gmx-users] Gromacs_GPU_Compiling_Problem Nikhil Maroli
[gmx-users] Gromacs_GPU_Compiling_Problem Peter Kroon
[gmx-users] Fwd: Residue 1 mapping problem? morpheus
[gmx-users] dielectric constant measurment Sajad Ahrari
[gmx-users] Related to fluctuation in Pressure ISHRAT JAHAN
[gmx-users] dielectric constant measurment Sajad Ahrari
[gmx-users] Fwd: Unusual bonding between residues in vmd ISHRAT JAHAN
[gmx-users] Related to fluctuation in Pressure Syed Azeem
[gmx-users] FEP calculations on multiple nodes Vikas Dubey
[gmx-users] Can I used slipids.ff + charmm36.ff to create a system? Carlos Navarro
[gmx-users] Can I used slipids.ff + charmm36.ff to create a system? Carlos Navarro
[gmx-users] Extract only last frame from a trr CLARK NICOLAS Joan
[gmx-users] Regarding indexing the atom labelled same in peptide Dilip H N
[gmx-users] RDF Dallas Warren
[gmx-users] RDF RAHUL SURESH
[gmx-users] RDF Dallas Warren
[gmx-users] RDF RAHUL SURESH
[gmx-users] installation_server machine_error Kashif
[gmx-users] installation_server machine_error Vytautas Rakeviius
[gmx-users] Missing values in enery EDR Sergio Manzetti
[gmx-users] Missing values in enery EDR Mark Abraham
[gmx-users] Can I use slipids.ff + charmm36.ff to create a system? Carlos Navarro
[gmx-users] Can I use slipids.ff + charmm36.ff to create a system? Carlos Navarro
[gmx-users] Can I use slipids.ff + charmm36.ff to create a system? Mark Abraham
[gmx-users] Can I use slipids.ff + charmm36.ff to create a system? Mark Abraham
[gmx-users] installation_server machine_error Mark Abraham
[gmx-users] Regarding indexing the atom labelled same in peptide Mark Abraham
[gmx-users] Regarding indexing the atom labelled same in peptide Mark Abraham
[gmx-users] Extract only last frame from a trr Mark Abraham
[gmx-users] Extract only last frame from a trr Mark Abraham
[gmx-users] Regarding Unknown cmap torsion between atoms Mark Abraham
[gmx-users] Can I use slipids.ff + charmm36.ff to create a system? Carlos Navarro
[gmx-users] 2nd CfP: From Virtual Reality to Immersive Analytics in Bioinformatics (SD&A 2018) Björn Sommer
[gmx-users] g_cluster Smolin, Nikolai
[gmx-users] Average and bfactors.pdb Justin Lemkul
[gmx-users] Fwd: Residue 1 mapping problem? Justin Lemkul
[gmx-users] Average and bfactors.pdb farial tavakoli
[gmx-users] g_cluster Erik Marklund
[gmx-users] FEP: mdp setting for mutation Alex Mathew
[gmx-users] Torsion analysis RAHUL SURESH
[gmx-users] Torsion analysis João Henriques
[gmx-users] Regarding Atom in residue XXX was not found in rtp entry with xxx atoms while sorting atoms Dilip H N
[gmx-users] FEP calculations on multiple nodes Vikas Dubey
[gmx-users] FEP calculations on multiple nodes Mark Abraham
[gmx-users] FEP calculations on multiple nodes Mark Abraham
[gmx-users] Regarding Atom in residue XXX was not found in rtp entry with xxx atoms while sorting atoms Mark Abraham
[gmx-users] Regarding Atom in residue XXX was not found in rtp entry with xxx atoms while sorting atoms Mark Abraham
[gmx-users] FEP calculations on multiple nodes Vikas Dubey
[gmx-users] FEP calculations on multiple nodes Mark Abraham
[gmx-users] FEP calculations on multiple nodes Leandro Bortot
[gmx-users] FEP calculations on multiple nodes Leandro Bortot
[gmx-users] FEP calculations on multiple nodes Mark Abraham
[gmx-users] FEP calculations on multiple nodes Vikas Dubey
[gmx-users] Gromacs simulation of two or more peptide chain Kalyanashis Jana
[gmx-users] FEP calculations on multiple nodes Mark Abraham
[gmx-users] FEP calculations on multiple nodes Mark Abraham
[gmx-users] pullx (gromacs 4.6 vs 2016) gromacs query
[gmx-users] gmx distance Sergio Manzetti
[gmx-users] GROMACS with Torque: Job stuck Souparno Adhikary
[gmx-users] gmx distance Vytautas Rakeviius
[gmx-users] GROMACS with Torque: Job stuck Vytautas Rakeviius
[gmx-users] GROMACS with Torque: Job stuck Mark Abraham
[gmx-users] Restraining molecule near interface Deepak Ojha
[gmx-users] GROMACS with Torque: Job stuck Souparno Adhikary
[gmx-users] GROMACS with Torque: Job stuck Mark Abraham
[gmx-users] gmx distance Tasneem Kausar
[gmx-users] gromacs error Neha Gupta
[gmx-users] QM/MM simulation Mostafa Javaheri
[gmx-users] finding Dihedrals with x2top Ali Shomali
[gmx-users] About the possibility of calculating dipole moment vectors of individual waters around polar solutes Sajeewa Pemasinghe
[gmx-users] Andersen thermostat with NPT - nstcomm < nstcalenergy Simon Kit Sang Chu
[gmx-users] Unable to install 5.1.14 Rajat Desikan
[gmx-users] ERROR IN EXECUTION ---GMX Neha Gupta
[gmx-users] ERROR IN EXECUTION ---GMX Nikhil Maroli
[gmx-users] ERROR IN EXECUTION ---GMX Neha Gupta
[gmx-users] ERROR IN EXECUTION ---GMX Nikhil Maroli
[gmx-users] ERROR IN EXECUTION ---GMX Neha Gupta
[gmx-users] Unable to install 5.1.14 Vytautas Rakeviius
[gmx-users] Unable to install 5.1.14 Vytautas Rakeviius
[gmx-users] gromacs error Vytautas Rakeviius
[gmx-users] QM/MM simulation (Mostafa Javaheri) Groenhof, Gerrit
[gmx-users] Trouble with gmx distance Vytautas Rakeviius
[gmx-users] ERROR IN EXECUTION ---GMX Tasneem Kausar
[gmx-users] Performance values Szilárd Páll
[gmx-users] Performance values Szilárd Páll
[gmx-users] Error with MPICH Szilárd Páll
[gmx-users] Trouble with gmx distance Sotirios Dionysios I. Papadatos
[gmx-users] problem installing plumed-2.3.2 spss4 at iacs.res.in
[gmx-users] problem installing plumed-2.3.2 Giovanni Bussi
[gmx-users] Corrupted checkpoint file from MD simulation Alexander Yang
[gmx-users] Corrupted checkpoint file from MD simulation melichercik at leaf.nh.cas.cz
[gmx-users] Surface Tension Calculation Lei
[gmx-users] RDF Dallas Warren
[gmx-users] RDF RAHUL SURESH
[gmx-users] gromacs error Neha Gupta
[gmx-users] Difference in Hydrogen Bond Lifetimes on truncating trajectory and also on using pbc Apramita Chand
[gmx-users] nstcomm < nstcalenergy Simon Kit Sang Chu
[gmx-users] Coordination vs cumulative number in gmx_rdf Dilip H N
[gmx-users] Difference in Hydrogen Bond Lifetimes on truncating trajectory and also on using pbc Erik Marklund
[gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa neha chaudhary
[gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa Nikhil Maroli
[gmx-users] nstcomm < nstcalenergy yujie liu
[gmx-users] nstcomm < nstcalenergy Justin Lemkul
[gmx-users] gromacs error Justin Lemkul
[gmx-users] Unable to install 5.1.14 Rajat Desikan
[gmx-users] Unable to install 5.1.14 Rajat Desikan
[gmx-users] gmx analyze Luzar analysis Valerio Ferrario
[gmx-users] gmx analyze Luzar analysis Erik Marklund
[gmx-users] Difference in Hydrogen Bond Lifetimes on truncating trajectory and also on using pbc Apramita Chand
[gmx-users] Difference in Hydrogen Bond Lifetimes on truncating trajectory and also on using pbc Erik Marklund
[gmx-users] gmx analyze Luzar analysis Valerio Ferrario
[gmx-users] Difference in hydrogen bond lifetimes with and without pbc Apramita Chand
[gmx-users] Surface tension for water Iman Ahmadabadi
[gmx-users] Surface tension for water Dan Gil
[gmx-users] Surface Tension Calculation Dan Gil
[gmx-users] pullx (gromacs 4.6 vs 2016) gromacs query
[gmx-users] Surface tension for water Iman Ahmadabadi
[gmx-users] Surface tension for water Dan Gil
[gmx-users] Surface tension for water Dan Gil
[gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa neha chaudhary
[gmx-users] Surface Tension Calculation Lei
[gmx-users] Surface tension for water Iman Ahmadabadi
[gmx-users] Surface tension for water Dan Gil
[gmx-users] Pure repulsive LJ potential for OPLSAA Lei
[gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa Nikhil Maroli
[gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa neha chaudhary
[gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa Nikhil Maroli
[gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa neha chaudhary
[gmx-users] Surface tension for water Iman Ahmadabadi
[gmx-users] Fwd: Difference in Hydrogen Bond Lifetimes on using pbc Apramita Chand
[gmx-users] Showing different RMSD values Seera Suryanarayana
[gmx-users] Showing different RMSD values Nikhil Maroli
[gmx-users] difference in potential energy Emran Heshmati
[gmx-users] gmxdump gmxcheck commands not found Apramita Chand
[gmx-users] Setting different intial velocities Apramita Chand
[gmx-users] possible bug in posre Sergio Manzetti
[gmx-users] difference in potential energy Justin Lemkul
[gmx-users] gmxdump gmxcheck commands not found Justin Lemkul
[gmx-users] Setting different intial velocities Justin Lemkul
[gmx-users] possible bug in posre Justin Lemkul
[gmx-users] possible bug in posre Sergio Manzetti
[gmx-users] possible bug in posre Justin Lemkul
[gmx-users] Surface tension for water André Farias de Moura
[gmx-users] triclinic box Niko Ukkonen
[gmx-users] triclinic box Hermann, Johannes
[gmx-users] possible bug in posre Sergio Manzetti
[gmx-users] possible bug in posre Justin Lemkul
[gmx-users] possible bug in posre Sergio Manzetti
[gmx-users] possible bug in posre Justin Lemkul
[gmx-users] Bug?! Lost particles while sorting Mohsen Ramezanpour
[gmx-users] Bug?! Lost particles while sorting Mohsen Ramezanpour
[gmx-users] Difference in Hydrogen Bond Lifetimes on using pbc Apramita Chand
[gmx-users] Bug?! Lost particles while sorting Mark Abraham
[gmx-users] Error regarding missing hydrogen atoms Vishal Pandya
[gmx-users] gmx mindist ‪Mohammad Roostaie‬ ‪
[gmx-users] RMSD Apramita Chand
[gmx-users] Fwd: Potential gradient in NVE simulation Saumyak Mukherjee
[gmx-users] Difference in hydrogen bond lifetimes with and without pbc Erik Marklund
[gmx-users] Gromacs simulation of two or more peptide chain Vytautas Rakeviius
[gmx-users] Gromacs simulation of two or more peptide chain Vytautas Rakeviius
[gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa neha chaudhary
[gmx-users] Bug?! Lost particles while sorting Mohsen Ramezanpour
[gmx-users] Bug?! Lost particles while sorting Mohsen Ramezanpour
[gmx-users] Symmetry corrections in FEP Dries Van Rompaey

Last message date: Thu Aug 31 22:38:58 CEST 2017
Archived on: Thu Aug 31 22:38:59 CEST 2017

Messages sorted by: [ thread ] [ subject ] [ author ]
More info on this list...

This archive was generated by Pipermail 0.09 (Mailman edition).