April 2020 Archives by thread
Starting: Wed Apr 1 02:05:57 CEST 2020
Ending: Thu Apr 30 20:07:50 CEST 2020
Messages: 472
- [gmx-users] Effect of atomic charge on bonding parameters
Neena Susan Eappen
- [gmx-users] How to reduce the penalty of small molecule from CGenFF
Justin Lemkul
- [gmx-users] Different force constants for different umbrella windows?
Justin Lemkul
- [gmx-users] 1-4 LJ interactions
Justin Lemkul
- [gmx-users] PCA analysis with different atoms in -s and -f
ZHANG Cheng
- [gmx-users] gmx rms divergence from the starting structure
Wei-Ta Li
- [gmx-users] distance from geometrical center of protein to the surface
Wei-Ta Li
- [gmx-users] 1 particles communicated to PME rank 3 are more than 2/3 times the cut-off out
Seketoulie Keretsu
- [gmx-users] Optimising mdrun
Robert Cordina
- [gmx-users] GROMACS mailing-list will move to a forum
Paul bauer
- [gmx-users] Problem with REST2
Joseph, Benjamin Philipp
- [gmx-users] Free energy of protonation
Gmx QA
- [gmx-users] Reviewing docking resluts
neelam wafa
- [gmx-users] Onsager coefficient
Sina Omrani
- [gmx-users] converting gromacs topology file to namd topology file
Hadi Rahmaninejad
- [gmx-users] Missing gromacs.lib when building Grmoacs 2020.1 in vs 2019
孙傲然
- [gmx-users] Issue with PMF
Alex
- [gmx-users] (no subject)
Feriel Terbeche
- [gmx-users] Simulation of Protein-Protein Complex
Surya Sanjay
- [gmx-users] Fwd: geometry optimization of metalloenzyme
Nadia Elghobashi-Meinhardt
- [gmx-users] Simulation of Protein-Protein Complex
Justin Lemkul
- [gmx-users] Fwd: no atom pairs for dispersion correction
Sadaf Rani
- [gmx-users] Scale Triclinic Box
Maryam Sadeghi
- [gmx-users] change the top file of a homodimer protein
Qasim Pars
- [gmx-users] How to parametrize a new molecule?
Herbert de Castro Georg
- [gmx-users] Calculate probability of presence of water around a residues
pooja kesari
- [gmx-users] How to use GROMACS license?
Nikhil Maroli
- [gmx-users] Unable to compile GROMACS 2020.1 using GNU 7.5.0
Wei-Tse Hsu
- [gmx-users] GROMACS 2020.1 failed to pass make check
Wei-Tse Hsu
- [gmx-users] Fumbling in the dark with dihedral pulling
Marko Petrovic
- [gmx-users] Bonds definition in itp files
Sina Omrani
- [gmx-users] Protonation state of aminoacids from pdb and pdb2gmx
Javier Luque Di Salvo
- [gmx-users] NAG N-Acetylglucosamine force field parameters
Javier Luque Di Salvo
- [gmx-users] Multi-GPU optimization, "DD without halo exchange is not supported"
Szilárd Páll
- [gmx-users] Anharmonic/Morse flexible water
Jacek Artur Kozuch
- [gmx-users] restarting a simulation
Sadaf Rani
- [gmx-users] Velocities from the .gro file
Mohamed Abdelaal
- [gmx-users] Simulate only one unit of the virus capsid while fixing its surrounding units
ZHANG Cheng
- [gmx-users] dt in mdp
Alex
- [gmx-users] Double-well potential for bonded interaction
Jacek Artur Kozuch
- [gmx-users] Dockerfile to use gromacs/gromacs in DockerHub?
fernando fuentes de la parra
- [gmx-users] Restarting a REST2 simulation
Joseph, Benjamin Philipp
- [gmx-users] Concatenating trajectories
Pandya, Akash
- [gmx-users] Converting a tpr file to an older version of gromacs
Mariem Ghoula
- [gmx-users] How to extend the force field by polariation parameters
Zuzana Benkova
- [gmx-users] Buggy 2020?
Parvez Mh
- [gmx-users] treating trajectory for diffusion calculations
Dave M
- [gmx-users] Regarding version of gromacs
Ashma Khan
- [gmx-users] GROMACS version issue
Yasaman KARAMI
- [gmx-users] Problem with pdb2gmx
Elham Taghikhani
- [gmx-users] Protonated ligand free energy calculation in water
Rolly Ng
- [gmx-users] segmentation fault gmx do_dssp
Sadaf Rani
- [gmx-users] energy minimizing
Afsane Farhadi
- [gmx-users] segmentation fault gmx do_dssp
Sadaf Rani
- [gmx-users] pdb2gmx: Selecting Force Field in first command
fernando at hypernetlabs.io
- [gmx-users] Regarding version of gromacs
Ashma Khan
- [gmx-users] Cannot run short-ranged nonbonded interactions on a GPU because there is none detected.
Mahmood Naderan
- [gmx-users] Problem with pdb2gmx
Elham Taghikhani
- [gmx-users] Problem in energy minimization step
Xuan Zhang
- [gmx-users] Post processing REMD simulation
Mohammad Madani
- [gmx-users] duplicate angle index- angle restraint
Sadaf Rani
- [gmx-users] duplicate angle index- angle restraint
Sadaf Rani
- [gmx-users] Electric field
Prithwish Nandi
- [gmx-users] how to run a MD of a small molecule in vacuum in Gromacs
Lazaro Castanedo
- [gmx-users] how to run a MD of a small molecule in vacuum in Gromacs
lazaro monteserin
- [gmx-users] how to run a MD of a small molecule in vacuum in Gromacs
lazaro monteserin
- [gmx-users] Triclinic box is too skewed
Jun Zhou
- [gmx-users] how to run a MD of a small molecule in vacuum in Gromacs
Neena Susan Eappen
- [gmx-users] Parametrization POM molecule
Paolo Costa
- [gmx-users] vdW cut-off to LJPME: Simulation crashes immediately
Udaya Dahal
- [gmx-users] Same one lipid in bilayer causing LINCS crashing during minimization
Erik Henze
- [gmx-users] about simulation of small molecules in vacuum. link to dropbox
lazaro monteserin
- [gmx-users] vdW cut-off to LJPME: Simulation crashes immediately
Udaya Dahal
- [gmx-users] Error message
Prithwish Nandi
- [gmx-users] how to run equilibration when freezing part of an small molecule in vacuum and in water environment?
lazaro monteserin
- [gmx-users] energy minimization
Afsane Farhadi
- [gmx-users] Polarization assistance request
Heroneme, Carl Joseph
- [gmx-users] Replica exchange probabilities beyond version 2016
Pritam Ganguly
- [gmx-users] Ways to calculate shear viscosity
Jun Zhou
- [gmx-users] Basic question about command line
Mohammad Madani
- [gmx-users] How to solve the "LINCS WARNING" problem
변진영
- [gmx-users] Basic question about command line (Mohammad Madani)
Teslim Olayiwola
- [gmx-users] gromacs 2020, bug? high total energy
Tamas Hegedus
- [gmx-users] How to prevent velocity generation for my position restrained molecules ?
Mohamed Abdelaal
- [gmx-users] semiisotropic pressure coupling.
Miro Astore
- [gmx-users] (NEW USER) Determining Complex Dielectric property of a solid state system
Tahsin Ashraf Khan
- [gmx-users] Can we implement NMR restraint data in Gromacs?
Chaturvedi Navneet
- [gmx-users] Error with Output from GMX cluster analysis
Teslim Olayiwola
- [gmx-users] Problem force constant bond stretc.
Paolo Costa
- [gmx-users] Trouble with restrained dihedrals
Marko Petrovic
- [gmx-users] GROMACS PBS GPU JOB submission
Tuanan Lourenço
- [gmx-users] Multi-GPU optimization, "DD without halo exchange is not supported"
Alan Gray
- [gmx-users] WARNING 1 [file topol.top, line 60334] - How to manage? -maxwarn 1 or any other solution
Adarsh V. K.
- [gmx-users] about problem running script for Gibbs free energy simulation
lazaro monteserin
- [gmx-users] Measuring bond distances, angles and dihedrals
Robert Cordina
- [gmx-users] Question on running gmx trjconv without 2 prompts
Lei Qian
- [gmx-users] Failed to find GROMACS magic number in trr frame header
Mijiddorj B
- [gmx-users] ' LONEPAIR LP1 ' gives error message in protein - ligand simulation
Adarsh V. K.
- [gmx-users] RIN (Residue interaction network) for protein ligand interactions
Prasanth G, Research Scholar
- [gmx-users] atomselection for index group of cyclic rings
Prasanth G, Research Scholar
- [gmx-users] atomtype "OE" in charmm36
Schirra, Simone
- [gmx-users] Appending crashed Replica Exchange Simulations: init_step/-replex is not equal for all subsystems
Johannes Hermann
- [gmx-users] How to solve the "LINCS WARNING" problem (???)
Prasanth G, Research Scholar
- [gmx-users] weird output from simultions of a protein between two sheets
Zuzana Benkova
- [gmx-users] position restrain of water
m g
- [gmx-users] Disabling MKL
Mahmood Naderan
- [gmx-users] Dramatic decrease NVE production
Dorj Bat
- [gmx-users] Does the energy minimization deals with velocity ?
Mohamed Abdelaal
- [gmx-users] Residue ‘XXX’ not found in residue topology database - SnCl6
Paolo Costa
- [gmx-users] Installation on iPad?
Ali Khodayari
- [gmx-users] Regarding use of harmonic wall model
Shashank Ranjan Srivastava
- [gmx-users] Failed to find GROMACS magic number in trr frame header
Mijiddorj B
- [gmx-users] Installation on iPad
Ali Khodayari
- [gmx-users] Artifact in pull-pbc-ref-prev-step-com
Alex
- [gmx-users] Question about Mean Square Displacement (MSD)
Sina Omrani
- [gmx-users] about correct methodology to run MD of small molecule in gromacs
lazaro monteserin
- [gmx-users] Triclinic box is too skewed
Jun Zhou
- [gmx-users] error in pdb2gmx
Sadaf Rani
- [gmx-users] error in pdb2gmx
Sadaf Rani
- [gmx-users] Segmentation fault (core dumped) error during minimization
Elham Taghikhani
- [gmx-users] Error in pdb2gmx
Sadaf Rani
- [gmx-users] Failed to find GROMACS magic number in trr frame header
Mijiddorj B
- [gmx-users] Problem with Potential Mean Force calculation
Rolly Ng
- [gmx-users] Regarding use of harmonic wall model
Shashank Ranjan Srivastava
- [gmx-users] Dihedral Restraints
Jacek Artur Kozuch
- [gmx-users] How to report bugs or issues?
Subhamoy Mahajan
- [gmx-users] How to report bugs or issues?
Yu Du
- [gmx-users] GROMACS mdp file for doing a single point energy after acpype conversion
ABEL Stephane
- [gmx-users] Problem C-H bonds of Benzene after minimization
Paolo Costa
- [gmx-users] GROMACS performance issues on POWER9/V100 node
Jonathan D. Halverson
- [gmx-users] GROMACS mdp file for doing a single point energy after acpype conversion
ABEL Stephane
- [gmx-users] about error running temperature equilibration
lazaro monteserin
- [gmx-users] Umbrella Sampling with 2 reaction coordinates
Ernesto Camparolla
- [gmx-users] COMPEL question: Channel filter outside membrane, how to orient compartment boundaries
Erik Henze
- [gmx-users] Periodic boundary conditions during the simulation
Mohamed Abdelaal
- [gmx-users] Regarding use of harmonic wall model
Shashank Ranjan Srivastava
- [gmx-users] gromacs.org_gmx-users Digest, Vol 192, Issue 89
Jun Zhou
- [gmx-users] Why there is no phosphorous atom in the "DA5" residue in dna.rtp
Tingguang.S
- [gmx-users] lincs warning
Afsane Farhadi
- [gmx-users] gromacs installation (2020&2019)
Netaly Khazanov
- [gmx-users] Fatal error pdb2gmx
Paolo Costa
- [gmx-users] Error No default Proper Dih. types
Paolo Costa
- [gmx-users] wham - Bootstraping
Alex
- [gmx-users] Atom CA used in that entry is not found in the input file
Daniel Burns
- [gmx-users] about how to create covar.ndx for dihedral Principal Component Analysis
lazaro monteserin
- [gmx-users] multiple nodes
Neha Gandhi
- [gmx-users] gmx sasa for protein-ligand complex(problem with command usage)
Archana Sonawani-Jagtap
- [gmx-users] lincs warning
Afsane Farhadi
- [gmx-users] Quick question: is TIP3P water model available in GROMOS54a7 force field?
Wei-Tse Hsu
- [gmx-users] [gmx users] Terminal amide hydrogens not included in H-bond analysis
Neena Susan Eappen
- [gmx-users] debugging
Miro Astore
- [gmx-users] Invalid atomtype format
Sadaf Rani
- [gmx-users] Atom positions change between topology generation and NVT mdrun
Max Winokan
- [gmx-users] Atom positions change between topology generation and NVT equilibration
Max Winokan
- [gmx-users] Atom positions change between topology generation and NVT equilibration
Max Winokan
- [gmx-users] POPC: Fatal error:
Dutta, Kunal
- [gmx-users] about segmentation fault related with gmx trjconv
lazaro monteserin
- [gmx-users] GROMACS TUTOR WANTED
Joel Subach
- [gmx-users] about how to create angle.index with specific angles
lazaro monteserin
- [gmx-users] sadaf rani shared "Atom_type_error files.zip" with you
sadaf rani (via Dropbox)
- [gmx-users] Invalid atomtype format (Justin Lemkul)
Sadaf Rani
- [gmx-users] sadaf rani shared "atomtypes.atp" with you
sadaf rani (via Dropbox)
- [gmx-users] Invalid atomtype format (Justin Lemkul
Sadaf Rani
- [gmx-users] GROMACS 2020.2 patch release available
Paul bauer
Last message date:
Thu Apr 30 20:07:50 CEST 2020
Archived on: Thu Apr 30 20:07:52 CEST 2020
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