April 2014 Archives by thread
Starting: Tue Apr 1 00:13:06 CEST 2014
Ending: Wed Apr 30 18:52:09 CEST 2014
Messages: 644
- [gmx-users] Water out of box? Negative Z-Coordinates
GtrAngus
- [gmx-users] difference in energy when using -nb cpu
Rafael I. Silverman y de la Vega
- [gmx-users] re difference between GPU and CPU only run
Rafael I. Silverman y de la Vega
- [gmx-users] Checking the possibility of one complex out of possible two
Pappu Kumar
- [gmx-users] about gromacs
Meenakshi Rajput
- [gmx-users] How to provide the FFTW3 install directory
Ly Minh Nhat
- [gmx-users] adding metal-bonding parameters to a force field
Ahmet yıldırım
- [gmx-users] gromacs
Meenakshi Rajput
- [gmx-users] Monitor GMX performance with CUDA
Dario Corrada
- [gmx-users] gromacs
Jernej Zidar
- [gmx-users] Erro in SMD simulation..
Kalyanashis
- [gmx-users] exclude some frames from trajectory
Saman Shahriyari
- [gmx-users] protein water contacts
pratibha
- [gmx-users] Checking the possibility of one complex out of possible two
Justin Lemkul
- [gmx-users] visualize gromacs trajectory in VMD
sunyeping
- [gmx-users] Projecting conformational changes onto PCs
Mendez Giraldez, Raul
- [gmx-users] Flat-bottom potentials
Andres Ortega
- [gmx-users] How deuterium order parameters computed?
Bin Liu
- [gmx-users] Error: illegal instruction (core dumped)
Ly Minh Nhat
- [gmx-users] drug-drug interaction energy
Manuel Azenha
- [gmx-users] MD simulations on a remote workstation
Amjad Farooq
- [gmx-users] extended bonds
pratibha
- [gmx-users] PMF from targeted MD vs. Umbrella Sampling/constraints
anaome
- [gmx-users] How to provide the FFTW3 install directory
kieuthu2212
- [gmx-users] all-bonds constraints
Juan Munoz-Garcia
- [gmx-users] GPU performance
pratibha
- [gmx-users] Conserved energy decreases linearly
David van der Spoel
- [gmx-users] Length of .xtc file in frames for C-Code
GtrAngus
- [gmx-users] all-bonds constraints
Juan Munoz-Garcia
- [gmx-users] segmentation fault on version 5.0 beta 2
Ly Minh Nhat
- [gmx-users] a gromacs feature to do TMD like simulation
Saman Shahriyari
- [gmx-users] Gromacs 5 umbrella sampling
Andres Ortega
- [gmx-users] MD with splitted system
davhak
- [gmx-users] Length of .xtc file in frames for C-Code
Barnett, James W.
- [gmx-users] Can Ryckaert-Bellemans(RB) function be used to calculate improper dihedrals?
CG
- [gmx-users] 1-D free energy plots using g_sham
richa
- [gmx-users] energy groups/GPU and 4.6 vs 5.0
michael.b
- [gmx-users] atom labeling in forcefield file and pdb are different
Sanchaita
- [gmx-users] how to create a PEO Residue database
Tom
- [gmx-users] how to create a PEO Residue database
michael.b
- [gmx-users] Regarding 1-d free energy profile from g_sham
richa
- [gmx-users] How to prevent box shrinking incessantly at x and y when doing membrane simulation using semiisotropic couple type?
CG
- [gmx-users] part2-adding metal-bonding parameters to a force field
Ahmet yıldırım
- [gmx-users] gromacs.org_gmx-users Digest, Vol 120, Issue 32
marzieh dehghan
- [gmx-users] glycated insulin (GROMACS)
marzieh dehghan
- [gmx-users] problem in simulation mutant p53 protein both in swiss pdb viewer and energy minimization with gromacs
delara aghaie
- [gmx-users] (no subject)
Meenakshi Rajput
- [gmx-users] Calculate heat capacity
maryam haji
- [gmx-users] Calculate heat capacity
maryam haji
- [gmx-users] atomtype c3 not found
Monoj Mon Kalita
- [gmx-users] The sum of the two largest charge group radii is larger than rlist
pratibha
- [gmx-users] atomtype c3 not found
Monoj Mon Kalita
- [gmx-users] [gmx-developers] modifying nonbonded interaction parameters
Justin Lemkul
- [gmx-users] How to redirect the calculation load toward GPU
Dario Corrada
- [gmx-users] First release candidate for GROMACS 5.0 is available
Mark Abraham
- [gmx-users] refcoord-scaling
Chetan Mahajan
- [gmx-users] Pull code stalling?
Justin Lemkul
- [gmx-users] Is something wrong wih my mdp?
chenxianli
- [gmx-users] possible configuration for gromacs gpu compute node
Harry Mark Greenblatt
- [gmx-users] My box size canges somehow
Vytautas
- [gmx-users] Trj_cavity segmentation fault
Rajeswari A.
- [gmx-users] How to redirect the calculation load toward GPU
Dario Corrada
- [gmx-users] Atomtype OW not found - spc water model
Carlos Navarrro Retamal
- [gmx-users] Cannot Generate CHARMM36 Topology for POPC with Virtual Sites
Chris Ing
- [gmx-users] Position restraint coordinates are missing
Yujie Wang
- [gmx-users] multiple peptides in the same box
maggin
- [gmx-users] problem in md run
Meenakshi Rajput
- [gmx-users] free energy caculation error
jane
- [gmx-users] Justin tutorial - V-rescale + Parinello-Rahman
Steven Neumann
- [gmx-users] Error in g_bar
bipin singh
- [gmx-users] energy components in g_energy
Yutian Yang
- [gmx-users] PG/PE 3:1 lipid bilayer
madhura khare
- [gmx-users] CHARMM36 force field available for GROMACS
gsettanni
- [gmx-users] the result of the free energy
jane
- [gmx-users] (no subject)
Nicola Staffolani
- [gmx-users] the result of the free energy
jane
- [gmx-users] Energy minimization result problem
neha_bharty
- [gmx-users] question about xvg file
Andrew Bostick
- [gmx-users] question about xvg file
Andrew Bostick
- [gmx-users] adding ATP parms to AMBER99
Stephen N. Floor
- [gmx-users] Waiting for protein-protein MD tutorial...Justin....!!!!
dhaval patel
- [gmx-users] No default U-B types in CHARMM36 FF
Albert
- [gmx-users] make_ndx, boolean operations
Dr. Vitaly Chaban
- [gmx-users] Position restraints and double precision
Miguel Caro
- [gmx-users] Determining interactions in Protein-Ligand complex simulations
MUSYOKA THOMMAS
- [gmx-users] How to do Monte Carlo in gmx
xiao
- [gmx-users] negative HB lifetime
Benrezkallah Djamila
- [gmx-users] g_select help
Deepak Ojha
- [gmx-users] g_chi-like analysis for nucleic acid residues
sbowerma
- [gmx-users] Segfault using Verlet-list with Gromacs 4.6.5 - MPI only
Sébastien Côté
- [gmx-users] Aromatic rings not plane after minimization
Pierre THEVENET
- [gmx-users] Ligand observables in a protein-ligand simulation
MUSYOKA THOMMAS
- [gmx-users] Degrees of freedom for each atom ?
diptipotdar
- [gmx-users] which forcefields are parametrized for implicit solvent models?
hanna pdb
- [gmx-users] g_current
Nilesh Dhumal
- [gmx-users] Potential for Frozen atoms
sukriti002
- [gmx-users] Vibrational spectrum from normal mode analysis - regd
ramesh cheerla
- [gmx-users] how to use g_angle to get the average dihedral angle ?
maggin
- [gmx-users] SDS parameters
Rebeca García Fandiño
- [gmx-users] SDS parameters
ABEL Stephane 175950
- [gmx-users] genconf of box of a few types of molecules
Valentina
- [gmx-users] Conserved Energy in csvr NVT runs
janos.daru
- [gmx-users] REMD, demux after 100 ns per replica
aperez
- [gmx-users] Number of contacts matrix
Raphael
- [gmx-users] Is there a tool for calculating mechanical properties of materials using GROMACS
xiaowu759
- [gmx-users] segmentation fault
Meenakshi Rajput
- [gmx-users] segmentation fault
Meenakshi Rajput
- [gmx-users] Fuse Protein and non Protein Part of Ligand
Archer
- [gmx-users] H-bond analysis
michael.b
- [gmx-users] Using GPU to do simulations
mircial at sjtu.edu.cn
- [gmx-users] pdb2gmx yielding (a couple of) -nan values for coordinates of built hydrogen atoms
Christopher Neale
- [gmx-users] Md simulation mdp options error
Ankita Naithani
- [gmx-users] Dipole moment calculations
Nilesh Dhumal
- [gmx-users] How to explain the phenomenon of -genbox?
maggin
- [gmx-users] mpirun error
maggin
- [gmx-users] Reproducibility in free energy calculations.
sujithkakkat .
- [gmx-users] about tutorial on virtual sites
sujithkakkat .
- [gmx-users] running parallel simulations on different of cores
Muthukumaran R
- [gmx-users] Specifying the number of OpenMP threads that g_hbond uses
Andrew DeYoung
- [gmx-users] how to fix center of mass
Tom
- [gmx-users] GCMC?
Tom
- [gmx-users] Verlet cut-off with shell
Mikhail Stukan
- [gmx-users] one initial configuration on two different system
Mahboobeh Eslami
- [gmx-users] Position Restraints with NVT and NPT
zanemarkson
- [gmx-users] Fwd: Concatenating two trajectories
sunita gupta
- [gmx-users] System coordinates not getting freezed
sukriti002
- [gmx-users] About cutoffs for OPLSAA
sujithkakkat .
- [gmx-users] Concatenating two trajectories
Monoj Mon Kalita
- [gmx-users] all-angles
Maria Astón Serrano
- [gmx-users] how to couple a organic molecule in water
xiao
- [gmx-users] g_potential help
rajat desikan
- [gmx-users] Cannot write trajectory frame; maybe you are out of disk space
Andrew Bostick
- [gmx-users] Brownian Dynamics
Yutian Yang
- [gmx-users] How to fix or constrain Center of Mass
Tom
- [gmx-users] Cannot write trajectory frame; maybe you are out of disk space
Andrew Bostick
- [gmx-users] [gmx-developers] Regarding Amber topology and co-ordinate file
Justin Lemkul
- [gmx-users] Using a forcefield from NAMD
Ali Khan
- [gmx-users] calculation speed of GROMACS and cut off parameters
mircial at sjtu.edu.cn
- [gmx-users] Cannot write trajectory frame; maybe you are out of disk space
Andrew Bostick
- [gmx-users] No default U-B types
Shima Arasteh
- [gmx-users] deprecating the Nabble forums
Rossen Apostolov
- [gmx-users] gromacs.org_gmx-users Digest, Vol 120, Issue 95
sunita gupta
- [gmx-users] Protein in energygrp_excl is not an energy group
Rebeca García Fandiño
- [gmx-users] Silica Nanoparticles
Kazem Sepehrinia
- [gmx-users] qmmm integration (g09)
g shomo
- [gmx-users] skipping the EM, NPT and NVT for re-run
Saman Shahriyari
- [gmx-users] Protein Ligand Interaction or Docking using Gromacs
neha_bharty
- [gmx-users] Non-neutral system
Ali Alizadeh
- [gmx-users] Non-neutral system
Ali Alizadeh
- [gmx-users] Special bond between metallic layers & protein
fantaman
- [gmx-users] problem with chimera opening gromacs 4.6.5 trajectories
Rafael I. Silverman y de la Vega
- [gmx-users] normal mode analysis - regd
ramesh cheerla
- [gmx-users] Com pulling in reverse Z direction in SMD simulation..
Kalyanashis
- [gmx-users] Cannot write trajectory frame; maybe you are out of disk space
Andrew Bostick
- [gmx-users] make install creating infinite recursive directories
Harry Mark Greenblatt
- [gmx-users] QM/MM simulations
Iamkaant
- [gmx-users] compilation issues with GCC/clang/CUDA on OSX
Stephen N. Floor
- [gmx-users] how to manipulate solute-solvent interactions in ff to get the correct solvation free energy?
Golshan Hejazi
- [gmx-users] skipping the EM, NPT and NVT for re-run
Justin Lemkul
- [gmx-users] High Pressure with Martini system
Ricardo O. S. Soares
- [gmx-users] NPT simulation stage
Mahboobeh Eslami
- [gmx-users] MD simullations with Morse potential
fantasticqhl
- [gmx-users] Cannot write trajectory frame; maybe you are out of disk space
Andrew Bostick
- [gmx-users] Help regarding potential energy
Gaurav Saraf IDD M Tech Biochem. Engg, IIT (BHU)
- [gmx-users] Cannot write trajectory frame; maybe you are out of disk space
Andrew Bostick
- [gmx-users] (no subject)
Swetha Srinivasan
- [gmx-users] NPT simulation stage
Justin Lemkul
- [gmx-users] (no subject)
Swetha Srinivasan
- [gmx-users] (no subject)
Swetha Srinivasan
- [gmx-users] g_dipoles
Nilesh Dhumal
- [gmx-users] SWCNT interaction with the outside of an ion channel
Andres Ortega
- [gmx-users] constraint center of mass
Tom
- [gmx-users] Converging the system to 300K and 1bar
Gaurav Saraf IDD M Tech Biochem. Engg, IIT (BHU)
- [gmx-users] LINCS warning
Gaurav Saraf IDD M Tech Biochem. Engg, IIT (BHU)
- [gmx-users] NPT simulation stage
Ali Alizadeh
- [gmx-users] NPT simulation stage
Mahboobeh Eslami
- [gmx-users] NPT simulation stage
Justin Lemkul
- [gmx-users] tabulated potentials - cutoff
Sabine Reisser
- [gmx-users] Azurin protein attached to metal atom of Cu.
Alessia Giuliani
- [gmx-users] define new bond
fantaman
- [gmx-users] Force magnitude in SMD pull_geometry options
Magdalena von Essen
- [gmx-users] Is viscosity increasing in the system due to the protein unfolding?
fatemeh ramezani
- [gmx-users] pdb2gmx, charmm22 and HEME
Erik Marklund
- [gmx-users] gromacs 5.0
gejingming
- [gmx-users] Write a pdb file after every ns of simulation
MUSYOKA THOMMAS
- [gmx-users] Azurin protein attached to metal atom of Cu.
Justin Lemkul
- [gmx-users] Amber to Gromacs
Nash, Anthony
- [gmx-users] Questions about g_energy output values Coul-SR, LJ-SR, Coul-14, LJ-14
Vytautas Rakeviius
Last message date:
Wed Apr 30 18:52:09 CEST 2014
Archived on: Wed Apr 30 18:52:11 CEST 2014
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