October 2019 Archives by thread

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Starting: Tue Oct 1 07:21:52 CEST 2019
Ending: Thu Oct 31 21:14:02 CET 2019
Messages: 308

• [gmx-users] Parameter preparation of non-standard amino acid   Mijiddorj B
• [gmx-users] Protein ligand simulation   DEEPANSHU SINGLA
  • [gmx-users] Protein ligand simulation   Najamuddin Memon
  • [gmx-users] Protein ligand simulation   Justin Lemkul
• [gmx-users] extracting trajectory using trjconv   Hadi Rahmaninejad
  • [gmx-users] extracting trajectory using trjconv   Chenyu Liu
    • [gmx-users] extracting trajectory using trjconv   Chenyu Liu
      • [gmx-users] extracting trajectory using trjconv   Hadi Rahmaninejad
      • [gmx-users] extracting trajectory using trjconv   Chenyu Liu
• [gmx-users] GROMACS 2019.4 patch release available   Paul bauer
• [gmx-users] how to calculate average structure   mmousivand93
• [gmx-users] Extracting trajectory   anupama sharma
  • [gmx-users] Extracting trajectory   Jorden Cabal
• [gmx-users] Simulation of membrane associated protein   Olga Press
  • [gmx-users] Simulation of membrane associated protein   Justin Lemkul
    • [gmx-users] Simulation of membrane associated protein   Olga Press
      • [gmx-users] Simulation of membrane associated protein   Justin Lemkul
      • [gmx-users] Simulation of membrane associated protein   Olga Press
• [gmx-users] charmm36M generated topology conversion to GROMOS54A7 ff   Yogesh Sharma
  • [gmx-users] charmm36M generated topology conversion to GROMOS54A7 ff   Justin Lemkul
• [gmx-users] Adding a new residue and Duplicate atom index () in angles error   Mijiddorj B
  • [gmx-users] Adding a new residue and Duplicate atom index () in angles error   Justin Lemkul
• [gmx-users] Understanding the gmx dipoles and gmx dielectric GROMACS functionality   Patel, Lara Anne
• [gmx-users] Unable to run gmx_mpi genion non-interactively   Sarah Lucas
  • [gmx-users] Unable to run gmx_mpi genion non-interactively   Chenyu Liu
  • [gmx-users] Unable to run gmx_mpi genion non-interactively   Justin Lemkul
• [gmx-users] Adding a new residue and Duplicate atom index () in angles error   Mijiddorj B
  • [gmx-users] Adding a new residue and Duplicate atom index () in angles error   Justin Lemkul
• [gmx-users] GROMACS Energy groups   Adip Jhaveri
  • [gmx-users] GROMACS Energy groups   Justin Lemkul
• [gmx-users] GROMACS 2018.8 patch release available   Paul bauer
• [gmx-users] Reg: Your suggestions for Gromacs simulation using a cofactor and a Zn ion together   Amit Jaiswal
  • [gmx-users] Reg: Your suggestions for Gromacs simulation using a cofactor and a Zn ion together   Justin Lemkul
• [gmx-users] Hydrogen Bond analysis   Pandya, Akash
  • [gmx-users] Hydrogen Bond analysis   Justin Lemkul
• [gmx-users] cut in gmx clustsize   Alex
  • [gmx-users] Fwd: cut in gmx clustsize   Alex
• [gmx-users] how to calculate average structure   mmousivand93
  • [gmx-users] how to calculate average structure   Subhomoi Borkotoky
    • [gmx-users] how to calculate average structure   mmousivand93
      • [gmx-users] how to calculate average structure   Subhomoi Borkotoky
• [gmx-users] increase number of lipids in 128popc.pdb   Yogesh Sharma
  • [gmx-users] increase number of lipids in 128popc.pdb   Justin Lemkul
• [gmx-users] RMSD analysis of protein-ligand complex   Quin K
  • [gmx-users] RMSD analysis of protein-ligand complex   Justin Lemkul
    • [gmx-users] RMSD analysis of protein-ligand complex   Quin K
      • [gmx-users] RMSD analysis of protein-ligand complex   Justin Lemkul
      • [gmx-users] RMSD analysis of protein-ligand complex   Quin K
      • [gmx-users] RMSD analysis of protein-ligand complex   Justin Lemkul
      • [gmx-users] RMSD analysis of protein-ligand complex   Quin K
      • [gmx-users] RMSD analysis of protein-ligand complex   Justin Lemkul
      • [gmx-users] RMSD analysis of protein-ligand complex   Quin K
      • [gmx-users] RMSD analysis of protein-ligand complex   Justin Lemkul
      • [gmx-users] RMSD analysis of protein-ligand complex   Quin K
      • [gmx-users] RMSD analysis of protein-ligand complex   Justin Lemkul
      • [gmx-users] RMSD analysis of protein-ligand complex   Quin K
• [gmx-users] Gromacs2019 + Gaussian09 QMMM   nikolaev at spbau.ru
• [gmx-users] warnings about tip3   Ayesha Fatima
  • [gmx-users] warnings about tip3   Justin Lemkul
• [gmx-users] Cellulose topology file   Iman Katouzian
• [gmx-users] Cellulose topology file   Iman Katouzian
  • [gmx-users] Cellulose topology file   Justin Lemkul
• [gmx-users] water deletor script error   Ayesha Fatima
  • [gmx-users] water deletor script error   Justin Lemkul
• [gmx-users] Protein ligand simulation   DEEPANSHU SINGLA
• [gmx-users] Pro-Lig Error   Iman Katouzian
  • [gmx-users] Pro-Lig Error   Najamuddin Memon
• [gmx-users] Solvation free energy and standard states   Wang Ruixing
• [gmx-users] How to perform a lipid bilayer MD simulation in Gromacs with mechanical stress?   laura pulido
• [gmx-users] [Performance] poor performance with NV V100   Jimmy Chen
  • [gmx-users] [Performance] poor performance with NV V100   Szilárd Páll
• [gmx-users] Solvation of protein on membrane surface .JPG   Olga Press (via Google Drive)
  • [gmx-users] Solvation of protein on membrane surface .JPG   Dallas Warren
• [gmx-users] Solvation of protein on membrane surface   Olga Press
  • [gmx-users] Solvation of protein on membrane surface   Justin Lemkul
    • [gmx-users] Solvation of protein on membrane surface   Olga Press
      • [gmx-users] Solvation of protein on membrane surface   Justin Lemkul
      • [gmx-users] Solvation of protein on membrane surface   Olga Press
• [gmx-users] Gromacs2019 + Gaussian09 QMMM (nikolaev at spbau.ru)   Groenhof, Gerrit
• [gmx-users] Implicit Solvent and Box Size   张 卓
  • [gmx-users] Implicit Solvent and Box Size   Paul bauer
• [gmx-users] Implicit Solvent and Box Size   张 卓
• [gmx-users] Implicit Solvent and Box Size   zhangzhuo10 at hotmail.com
  • [gmx-users] Implicit Solvent and Box Size   Justin Lemkul
• [gmx-users] Shape of the aggregate   Aishwarya Dhar
  • [gmx-users] Shape of the aggregate   Dallas Warren
• [gmx-users] Implicit Solvent and Box Size   zhangzhuo10 at hotmail.com
  • [gmx-users] 回复: Re: Implicit Solvent and Box Size   张 卓
    • [gmx-users] 回复: Re: Implicit Solvent and Box Size   Justin Lemkul
    • [gmx-users] 回复: 回复: Re: Implicit Solvent and Box Size   Zhang Zhuo
      • [gmx-users] �ظ�: �ظ�: Re: Implicit Solvent and Box Size   John Whittaker
• [gmx-users] Need help with installation of Gromacs-2019.3 with Intell compilers   Lyudmyla Dorosh
  • [gmx-users] Need help with installation of Gromacs-2019.3 with Intell compilers   Paul bauer
    • [gmx-users] Need help with installation of Gromacs-2019.3 with Intell compilers   Lyudmyla Dorosh
• [gmx-users] Protein ligand simulation topology   DEEPANSHU SINGLA
  • [gmx-users] Protein ligand simulation topology   Justin Lemkul
• [gmx-users] ERROR :: Atomtype LC3 not found : KALP-15 in water tutorial   Seketoulie Keretsu
  • [gmx-users] ERROR :: Atomtype LC3 not found : KALP-15 in water tutorial   Justin Lemkul
• [gmx-users] INFLATEGRO SHRINKING SCRIPT ERROR   Yogesh Sharma
• [gmx-users] how to cluster protein conformations obtained from different trajectories?   rajat punia
  • [gmx-users] how to cluster protein conformations obtained from different trajectories?   Justin Lemkul
    • [gmx-users] how to cluster protein conformations obtained from different trajectories?   rajat punia
• [gmx-users] "Re: Shape of the aggregate (Dallas Warren)"   Aishwarya Dhar
  • [gmx-users] "Re: Shape of the aggregate (Dallas Warren)"   Aishwarya Dhar
    • [gmx-users] "Re: Shape of the aggregate (Dallas Warren)"   Dallas Warren
• [gmx-users] Understanding the gmx dipoles and gmx dielectric GROMACS functionality   Patel, Lara Anne
• [gmx-users] cpt file   Alex
  • [gmx-users] cpt file   Justin Lemkul
• [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation   Amit Jaiswal
  • [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation   Jorden Cabal
    • [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation   Amit Jaiswal
      • [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation   Amit Jaiswal
      • [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation   Jorden Cabal
      • [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation   Amit Jaiswal
      • [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation   Jorden Cabal
      • [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation   ISHRAT JAHAN
      • [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation   Justin Lemkul
      • [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation   Amit Jaiswal
      • [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation   Jorden Cabal
      • [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation   Amit Jaiswal
      • [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation   Jorden Cabal
      • [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation   Justin Lemkul
      • [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation   Amit Jaiswal
      • [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation   Justin Lemkul
• [gmx-users] Error running gromacs tutorial   Suprim Tha
  • [gmx-users] Error running gromacs tutorial   antonia vyrkou
    • [gmx-users] Error running gromacs tutorial   wangyue2018 at lzu.edu.cn
      • [gmx-users] Error running gromacs tutorial   Suprim Tha
• [gmx-users] Help with pull code for umbrella pulling   Slabbert, B, Mr [bslabbert at sun.ac.za]
• [gmx-users] Help with a failing test - gromacs 2019.4 - Test 42   Raymond Arter
  • [gmx-users] Help with a failing test - gromacs 2019.4 - Test 42   Szilárd Páll
    • [gmx-users] Help with a failing test - gromacs 2019.4 - Test 42   Raymond Arter
• [gmx-users] Gromacs tutorial   Suprim Tha
  • [gmx-users] Gromacs tutorial   Justin Lemkul
  • [gmx-users] Gromacs tutorial   Nidhi singh
    • [gmx-users] Gromacs tutorial   Suprim Tha
      • [gmx-users] Gromacs tutorial   Justin Lemkul
      • [gmx-users] Gromacs tutorial   Suprim Tha
      • [gmx-users] Gromacs tutorial   Suprim Tha
      • [gmx-users] Gromacs tutorial   Suprim Tha
      • [gmx-users] Gromacs tutorial   Justin Lemkul
• [gmx-users] Solid surface simulation and PBC issues   Samuel Asante Afari
  • [gmx-users] Solid surface simulation and PBC issues   Benson Muite
• [gmx-users] simulating glass materials using GROMACS   Alex Mathew
  • [gmx-users] simulating glass materials using GROMACS   paul buscemi
• [gmx-users] Error in cgenff   Suprim Tha
  • [gmx-users] Error in cgenff   Justin Lemkul
• [gmx-users] Concentration gradient across bilayer   Yogesh Sharma
• [gmx-users] Question about gmx_wham   Alexander Phillips
  • [gmx-users] Question about gmx_wham   John Whittaker
    • [gmx-users] Question about gmx_wham   Alexander Phillips
• [gmx-users] Concentration gradient across bilayer   Nikhil Maroli
• [gmx-users] Implementing Hamiltonian replica exchange simulations   Searle Duay
  • [gmx-users] Implementing Hamiltonian replica exchange simulations   Justin Lemkul
    • [gmx-users] Implementing Hamiltonian replica exchange simulations   Searle Duay
      • [gmx-users] Implementing Hamiltonian replica exchange simulations   Matthew Fisher
      • [gmx-users] Implementing Hamiltonian replica exchange simulations   Searle Duay
      • [gmx-users] Implementing Hamiltonian replica exchange simulations   Michael Shirts
• [gmx-users] [Performance] poor performance with NV V100   Szilárd Páll
• [gmx-users] shift in trajectory   Amin Rouy
  • [gmx-users] shift in trajectory   Patel, Lara Anne
    • [gmx-users] shift in trajectory   Justin Lemkul
      • [gmx-users] shift in trajectory   Amin Rouy
      • [gmx-users] shift in trajectory   Justin Lemkul
      • [gmx-users] shift in trajectory   Amin Rouy
      • [gmx-users] shift in trajectory   Justin Lemkul
      • [gmx-users] shift in trajectory   Amin Rouy
      • [gmx-users] shift in trajectory   Justin Lemkul
  • [gmx-users] shift in trajectory   Patel, Lara Anne
    • [gmx-users] shift in trajectory   Justin Lemkul
• [gmx-users] Normal Mode Analysis   Adip Jhaveri
  • [gmx-users] Normal Mode Analysis   David van der Spoel
    • [gmx-users] Normal Mode Analysis   Adip Jhaveri
• [gmx-users] distance analysis error   Mario Andres Rodriguez Pineda
  • [gmx-users] distance analysis error   Dallas Warren
    • [gmx-users] distance analysis error   Mario Andres Rodriguez Pineda
• [gmx-users] Question about default auto setting of mdrun -pin   Kutzner, Carsten
• [gmx-users] Fatal Error when launching gromacs 2019.2 on GPU.   Artem Shekhovtsov
  • [gmx-users] Fatal Error when launching gromacs 2019.2 on GPU.   Szilárd Páll
  • [gmx-users] Fatal Error when launching gromacs 2019.2 on GPU.   Szilárd Páll
    • [gmx-users] Fatal Error when launching gromacs 2019.2 on GPU.   Artem Shekhovtsov
      • [gmx-users] Fatal Error when launching gromacs 2019.2 on GPU.   Szilárd Páll
• [gmx-users] Hydrogens of ATB ligand show obvious vibration under all-bonds contraints?   Du, Yu
  • [gmx-users] Hydrogens of ATB ligand show obvious vibration under all-bonds contraints?   Justin Lemkul
    • [gmx-users] Hydrogens of ATB ligand show obvious vibration under all-bonds contraints?   Du, Yu
      • [gmx-users] Hydrogens of ATB ligand show obvious vibration under all-bonds contraints?   Du, Yu
      • [gmx-users] Hydrogens of ATB ligand show obvious vibration under all-bonds contraints?   Billy Williams-Noonan
      • [gmx-users] Hydrogens of ATB ligand show obvious vibration under all-bonds contraints?   Du, Yu
      • [gmx-users] Hydrogens of ATB ligand show obvious vibration under all-bonds contraints?   Billy Williams-Noonan
• [gmx-users] Calculation for PMF, Wham error   Rabeta Yeasmin
  • [gmx-users] Calculation for PMF, Wham error   Justin Lemkul
• [gmx-users] Fatal error: no domain decomposition   Patricia Saenz Méndez
  • [gmx-users] Fatal error: no domain decomposition   Justin Lemkul
    • [gmx-users] Fatal error: no domain decomposition   Patricia Saenz Méndez
• [gmx-users] Question about default auto setting of mdrun -pin   aeszter at gwdg.de
  • [gmx-users] Question about default auto setting of mdrun -pin   Szilárd Páll
    • [gmx-users] Question about default auto setting of mdrun -pin   aeszter at gwdg.de
• [gmx-users] Coarse-grained MD   Shan Jayasinghe
• [gmx-users] Changing the default cuda path   Mahmood Naderan
• [gmx-users] Problem on pbc atom   Mahsa Rezaei
  • [gmx-users] Problem on pbc atom   Justin Lemkul
• [gmx-users] regression test errors   Dave M
  • [gmx-users] regression test errors   Dave M
    • [gmx-users] regression test errors   Paul Bauer
      • [gmx-users] regression test errors   Dave M
      • [gmx-users] regression test errors   Paul Bauer
      • [gmx-users] regression test errors   Dave M
      • [gmx-users] regression test errors   Paul bauer
      • [gmx-users] regression test errors   Dave M
      • [gmx-users] regression test errors   Paul bauer
      • [gmx-users] regression test errors   Dave M
• [gmx-users] Advice for free energy perturbation calculations   Raphaël Robidas
• [gmx-users] Intermolecular Nonbonded Interactions   Batuhan Kav
  • [gmx-users] Intermolecular Nonbonded Interactions   Justin Lemkul
• [gmx-users] GROMACS showing error   Szilárd Páll
• [gmx-users] Frozen group moves!   Alex
  • [gmx-users] Frozen group moves!   David van der Spoel
    • [gmx-users] Frozen group moves!   Alex
• [gmx-users] surface energy for polymer boxes   Maria Luisa
• [gmx-users] Tabulate potential   Tam, Benjamin
• [gmx-users] supercell   Alex
  • [gmx-users] supercell   Dallas Warren
• [gmx-users] setting up osmotic gradient across bilayer.   Yogesh Sharma
  • [gmx-users] setting up osmotic gradient across bilayer.   Dallas Warren
• [gmx-users] calculation of tilt angle of head groups of lipid   SHAHEE ISLAM
• [gmx-users] Define intermolecular interactions in L-J simulation   Li, Shi
  • [gmx-users] Define intermolecular interactions in L-J simulation   Justin Lemkul
  • [gmx-users] Define intermolecular interactions in L-J simulation   David van der Spoel
• [gmx-users] QM/MM run tips or tutorials   Bogdanov, Vladimir
• [gmx-users] setting up osmotic gradient across bilayer.   Yogesh Sharma
  • [gmx-users] setting up osmotic gradient across bilayer.   Dallas Warren
• [gmx-users] Define intermolecular interactions in L-J simulation   Li, Shi
• [gmx-users] Average structure from trajectory   Jacek Artur Kozuch
  • [gmx-users] Average structure from trajectory   Edward Francisco Mendez Otalvaro
• [gmx-users] QM/MM run tips or tutorials (Bogdanov, Vladimir)   Groenhof, Gerrit
• [gmx-users] how to select head groups of lipid within 10 angstrom of protein   SHAHEE ISLAM
  • [gmx-users] how to select head groups of lipid within 10 angstrom of protein   Peter Stern
    • [gmx-users] how to select head groups of lipid within 10 angstrom of protein   Justin Lemkul
      • [gmx-users] how to select head groups of lipid within 10 angstrom of protein   SHAHEE ISLAM
      • [gmx-users] how to select head groups of lipid within 10 angstrom of protein   SHAHEE ISLAM
• [gmx-users] Obtaining stress-strain curves: Parrinello-Rahman, anisotropic and deform   Nigel Hew
• [gmx-users] gmx rdf not reading gmx checked trr file.   Jones de Andrade
• [gmx-users] Temperature coupling group and center-of-mass (COM) motion removal in simulation of protein on membrane surface   Olga Press
• [gmx-users] Non-zero total charge   shyama murali
  • [gmx-users] Non-zero total charge   Jones de Andrade
• [gmx-users] gmx trjcat   Alex
  • [gmx-users] Fwd: gmx trjcat   Alex
    • [gmx-users] Fwd: gmx trjcat   Paul bauer
      • [gmx-users] Fwd: gmx trjcat   Justin Lemkul
      • [gmx-users] Fwd: gmx trjcat   Alex
      • [gmx-users] Fwd: gmx trjcat   Justin Lemkul
      • [gmx-users] Fwd: gmx trjcat   Paul bauer
      • [gmx-users] Fwd: gmx trjcat   Alex
      • [gmx-users] Fwd: gmx trjcat   Elton Carvalho
• [gmx-users] How to run on cluster   Shradheya R.R. Gupta
• [gmx-users] How to run on cluster   Shradheya R.R. Gupta
• [gmx-users] Pressure outputs from gmx energy   Anh Vo
  • [gmx-users] Pressure outputs from gmx energy   Justin Lemkul
• [gmx-users] Fwd:   saranya
  • [gmx-users] Fwd:   Justin Lemkul
• [gmx-users] strange structure after energy minimization   Albert
  • [gmx-users] strange structure after energy minimization   Justin Lemkul
    • [gmx-users] strange structure after energy minimization   Albert
• [gmx-users] NVT equilibration of protein on membrane surface   Olga Press
  • [gmx-users] NVT equilibration of protein on membrane surface   Justin Lemkul
    • [gmx-users] NVT equilibration of protein on membrane surface   Olga Press
      • [gmx-users] NVT equilibration of protein on membrane surface   Justin Lemkul
      • [gmx-users] NVT equilibration of protein on membrane surface   Olga Press
      • [gmx-users] NVT equilibration of protein on membrane surface   Justin Lemkul
      • [gmx-users] NVT equilibration of protein on membrane surface   Olga Press
      • [gmx-users] NVT equilibration of protein on membrane surface   Justin Lemkul
• [gmx-users] defining parameters in a separate itp file   Dave M
  • [gmx-users] defining parameters in a separate itp file   Dallas Warren
  • [gmx-users] defining parameters in a separate itp file   Justin Lemkul
    • [gmx-users] defining parameters in a separate itp file   Dave M
      • [gmx-users] defining parameters in a separate itp file   Justin Lemkul
      • [gmx-users] defining parameters in a separate itp file   Dave M
• [gmx-users] Reg: GPU use   Bidhan Chandra Garain
  • [gmx-users] Reg: GPU use   Szilárd Páll
• [gmx-users] error in Umbrella sampling   Bratin Kumar Das
  • [gmx-users] error in Umbrella sampling   John Whittaker
• [gmx-users] Creating distance restraints between two atoms of different molecules   Mustafa Tekpinar
  • [gmx-users] Creating distance restraints between two atoms of different molecules   Justin Lemkul
    • [gmx-users] Creating distance restraints between two atoms of different molecules   Mustafa Tekpinar
• [gmx-users] how to perform analysis in faster with multicore/processor   Nikhil Maroli
  • [gmx-users] how to perform analysis in faster with multicore/processor   Christian Blau
    • [gmx-users] how to perform analysis in faster with multicore/processor   Justin Lemkul
• [gmx-users] Facing problem to generate .tpr file   rakesh parida
  • [gmx-users] Facing problem to generate .tpr file   Justin Lemkul
• [gmx-users] Simulated Annealing General Procedure   Neena Susan Eappen
• [gmx-users] error   Vidhu Agrawal
  • [gmx-users] error   Dallas Warren
• [gmx-users] error   Vidhu Agrawal
  • [gmx-users] error   Dallas Warren
• [gmx-users] regarding rmsd calculaton   shakuntala dhurua
  • [gmx-users] regarding rmsd calculaton   rajat punia
    • [gmx-users] regarding rmsd calculaton   shakuntala dhurua
      • [gmx-users] regarding rmsd calculaton   Justin Lemkul
      • [gmx-users] regarding rmsd calculaton   shakuntala dhurua
      • [gmx-users] regarding rmsd calculaton   Justin Lemkul
• [gmx-users] error   Vidhu Agrawal
  • [gmx-users] error   Justin Lemkul
• [gmx-users] Works well on CPU, not on GPU   Alex

Last message date: Thu Oct 31 21:14:02 CET 2019
Archived on: Thu Oct 31 21:14:04 CET 2019

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