October 2019 Archives by subject

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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] "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] [Performance] poor performance with NV V100 Jimmy Chen
[gmx-users] [Performance] poor performance with NV V100 Szilárd Páll
[gmx-users] [Performance] poor performance with NV V100 Szilárd Páll
[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] 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] Advice for free energy perturbation calculations Raphaël Robidas
[gmx-users] Average structure from trajectory Jacek Artur Kozuch
[gmx-users] Average structure from trajectory Edward Francisco Mendez Otalvaro
[gmx-users] Calculation for PMF, Wham error Rabeta Yeasmin
[gmx-users] Calculation for PMF, Wham error Justin Lemkul
[gmx-users] calculation of tilt angle of head groups of lipid SHAHEE ISLAM
[gmx-users] Cellulose topology file Iman Katouzian
[gmx-users] Cellulose topology file Iman Katouzian
[gmx-users] Cellulose topology file Justin Lemkul
[gmx-users] Changing the default cuda path Mahmood Naderan
[gmx-users] charmm36M generated topology conversion to GROMOS54A7 ff Yogesh Sharma
[gmx-users] charmm36M generated topology conversion to GROMOS54A7 ff Justin Lemkul
[gmx-users] Coarse-grained MD Shan Jayasinghe
[gmx-users] Concentration gradient across bilayer Yogesh Sharma
[gmx-users] Concentration gradient across bilayer Nikhil Maroli
[gmx-users] cpt file Alex
[gmx-users] cpt file Justin Lemkul
[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] cut in gmx clustsize Alex
[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] Define intermolecular interactions in L-J simulation Li, Shi
[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] 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] error Vidhu Agrawal
[gmx-users] error Vidhu Agrawal
[gmx-users] error Dallas Warren
[gmx-users] error Dallas Warren
[gmx-users] error Vidhu Agrawal
[gmx-users] error 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] Error in cgenff Suprim Tha
[gmx-users] Error in cgenff Justin Lemkul
[gmx-users] error in Umbrella sampling Bratin Kumar Das
[gmx-users] error in Umbrella sampling John Whittaker
[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] Extracting trajectory anupama sharma
[gmx-users] Extracting trajectory Jorden Cabal
[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] Facing problem to generate .tpr file rakesh parida
[gmx-users] Facing problem to generate .tpr file Justin Lemkul
[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. 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] 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] Frozen group moves! Alex
[gmx-users] Frozen group moves! David van der Spoel
[gmx-users] Frozen group moves! Alex
[gmx-users] Fwd: saranya
[gmx-users] Fwd: Justin Lemkul
[gmx-users] Fwd: cut in gmx clustsize 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] gmx rdf not reading gmx checked trr file. Jones de Andrade
[gmx-users] gmx trjcat Alex
[gmx-users] GROMACS 2018.8 patch release available Paul bauer
[gmx-users] GROMACS 2019.4 patch release available Paul bauer
[gmx-users] GROMACS Energy groups Adip Jhaveri
[gmx-users] GROMACS Energy groups Justin Lemkul
[gmx-users] GROMACS showing error Szilárd Páll
[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] Gromacs2019 + Gaussian09 QMMM nikolaev at spbau.ru
[gmx-users] Gromacs2019 + Gaussian09 QMMM (nikolaev at spbau.ru) Groenhof, Gerrit
[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] Help with pull code for umbrella pulling Slabbert, B, Mr [bslabbert at sun.ac.za]
[gmx-users] how to calculate average structure mmousivand93
[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] 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] How to perform a lipid bilayer MD simulation in Gromacs with mechanical stress? laura pulido
[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] How to run on cluster Shradheya R.R. Gupta
[gmx-users] How to run on cluster Shradheya R.R. Gupta
[gmx-users] How to run on cluster Shradheya R.R. Gupta
[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] Hydrogen Bond analysis Pandya, Akash
[gmx-users] Hydrogen Bond analysis 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? 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] Implementing Hamiltonian replica exchange simulations Matthew Fisher
[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 Searle Duay
[gmx-users] Implementing Hamiltonian replica exchange simulations Michael Shirts
[gmx-users] Implementing Hamiltonian replica exchange simulations Searle Duay
[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] Implicit Solvent and Box Size zhangzhuo10 at hotmail.com
[gmx-users] increase number of lipids in 128popc.pdb Yogesh Sharma
[gmx-users] increase number of lipids in 128popc.pdb Justin Lemkul
[gmx-users] INFLATEGRO SHRINKING SCRIPT ERROR Yogesh Sharma
[gmx-users] Intermolecular Nonbonded Interactions Batuhan Kav
[gmx-users] Intermolecular Nonbonded Interactions Justin Lemkul
[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] Need help with installation of Gromacs-2019.3 with Intell compilers Lyudmyla Dorosh
[gmx-users] Non-zero total charge shyama murali
[gmx-users] Non-zero total charge Jones de Andrade
[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] 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] Obtaining stress-strain curves: Parrinello-Rahman, anisotropic and deform Nigel Hew
[gmx-users] Parameter preparation of non-standard amino acid Mijiddorj B
[gmx-users] Pressure outputs from gmx energy Anh Vo
[gmx-users] Pressure outputs from gmx energy Justin Lemkul
[gmx-users] Pro-Lig Error Iman Katouzian
[gmx-users] Pro-Lig Error Najamuddin Memon
[gmx-users] Problem on pbc atom Mahsa Rezaei
[gmx-users] Problem on pbc atom Justin Lemkul
[gmx-users] Protein ligand simulation DEEPANSHU SINGLA
[gmx-users] Protein ligand simulation Najamuddin Memon
[gmx-users] Protein ligand simulation Justin Lemkul
[gmx-users] Protein ligand simulation DEEPANSHU SINGLA
[gmx-users] Protein ligand simulation topology DEEPANSHU SINGLA
[gmx-users] Protein ligand simulation topology Justin Lemkul
[gmx-users] QM/MM run tips or tutorials Bogdanov, Vladimir
[gmx-users] QM/MM run tips or tutorials (Bogdanov, Vladimir) Groenhof, Gerrit
[gmx-users] Question about default auto setting of mdrun -pin Kutzner, Carsten
[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] Question about gmx_wham Alexander Phillips
[gmx-users] Question about gmx_wham John Whittaker
[gmx-users] Question about gmx_wham Alexander Phillips
[gmx-users] Reg: GPU use Bidhan Chandra Garain
[gmx-users] Reg: GPU use Szilárd Páll
[gmx-users] Reg: GPU use Szilárd Páll
[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] 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 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 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 Justin Lemkul
[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 Justin Lemkul
[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] 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] 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] setting up osmotic gradient across bilayer. Yogesh Sharma
[gmx-users] setting up osmotic gradient across bilayer. Dallas Warren
[gmx-users] setting up osmotic gradient across bilayer. Yogesh Sharma
[gmx-users] setting up osmotic gradient across bilayer. Dallas Warren
[gmx-users] Shape of the aggregate Aishwarya Dhar
[gmx-users] Shape of the aggregate Dallas Warren
[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 Patel, Lara Anne
[gmx-users] shift in trajectory Justin Lemkul
[gmx-users] shift in trajectory Patel, Lara Anne
[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] Simulated Annealing General Procedure Neena Susan Eappen
[gmx-users] simulating glass materials using GROMACS Alex Mathew
[gmx-users] simulating glass materials using GROMACS paul buscemi
[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] Solid surface simulation and PBC issues Samuel Asante Afari
[gmx-users] Solid surface simulation and PBC issues Benson Muite
[gmx-users] Solvation free energy and standard states Wang Ruixing
[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] 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] 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] supercell Alex
[gmx-users] supercell Dallas Warren
[gmx-users] surface energy for polymer boxes Maria Luisa
[gmx-users] Tabulate potential Tam, Benjamin
[gmx-users] Temperature coupling group and center-of-mass (COM) motion removal in simulation of protein on membrane surface Olga Press
[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] Understanding the gmx dipoles and gmx dielectric GROMACS functionality Patel, Lara Anne
[gmx-users] Understanding the gmx dipoles and gmx dielectric GROMACS functionality Patel, Lara Anne
[gmx-users] warnings about tip3 Ayesha Fatima
[gmx-users] warnings about tip3 Justin Lemkul
[gmx-users] water deletor script error Ayesha Fatima
[gmx-users] water deletor script error Justin Lemkul
[gmx-users] Works well on CPU, not on GPU Alex
[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

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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