[gmx-users] Error during PUMED installation for GROMACS-4.5.3

Hello, I am getting following error while installing PLUMED for gromacs Please suggest if someone has succesfully installed PLUMED on GROMACS-4.5.3. The error is as below: --- root@bipin-OptiPlex-330:/usr/lo

[gmx-users] Re: adding ff parameter of modified residue to charmm ff

Hi, I followed the tutorial - http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field for updating the Charmm FF for my modified residue .. I added the residues to the .rtp file , then I added the new atom types in .atp file , The compound has some linkage with serine and

Re: [gmx-users] oplsaa galactose

Hi, I am trying to simulate hexopyronase using OPLS-AA forcefield using parameters from the paper: An improved OPLS?AA force field for carbohydrates, 2002 by Gunsteren. The set of torsional angle parameters in the paper are given in Kcal/mol, but because I am using OPLS-AA I would need to

Re: [gmx-users] Particle type 'B' in topology file?

cdalgicdir wrote: Hi all, I have performed a simulation where for an atomtype, I accidentally put 'B' instead of 'A' which stands for 'atom'. The manual doesn't mention any 'B''s for particle type, (it mentions A,S,V and D). I have then corrected this (replaced B with A) and obtained a tota

Re: [gmx-users] mpi run in Gromacs

On 2/03/2011 11:37 PM, Erik Marklund wrote: Selina Nawaz skrev 2011-03-02 11.54: Hi, I am a Phd student studying polymer membranes. I have installed Gromacs version 4.5.2 on our department cluster and attempted to run a simulations on a DPPC bilayer membranes taken from the tielleman website.

[gmx-users] Particle type 'B' in topology file?

Hi all, I have performed a simulation where for an atomtype, I accidentally put 'B' instead of 'A' which stands for 'atom'. The manual doesn't mention any 'B''s for particle type, (it mentions A,S,V and D). I have then corrected this (replaced B with A) and obtained a totally different config

Re: [gmx-users] Re: Polarizable halide (Iodide)

On 2011-03-02 09.44, Mikhail Stukan wrote: David, What should not be working in the current version? Do you mean that any polarizable model (water for example) can run on a single processor only? I am currently using the model by Roux et al. for NaCl solution in SWM4-NDP model and everything s

Re: [gmx-users] mpi run in Gromacs

Selina Nawaz skrev 2011-03-02 11.54: Hi, I am a Phd student studying polymer membranes. I have installed Gromacs version 4.5.2 on our department cluster and attempted to run a simulations on a DPPC bilayer membranes taken from the tielleman website. I have set the system up in an NPT ensemble

[gmx-users] water residence time on a certain group of ligand

Dear gromacs users, I want to calculate water molecules residence time on a certain groups of a ligand. I found in gromacs exercises how to do it: https://extras.csc.fi/chem/courses/gmx2004/exercises/index.html To get water residence time I need: 1) Obtain hbac.xvg, using this command: g_hbond -c

[gmx-users] mpi run in Gromacs

Hi, I am a Phd student studying polymer membranes. I have installed Gromacs version 4.5.2 on our department cluster and attempted to run a simulations on a DPPC bilayer membranes taken from the tielleman website. I have set the system up in an NPT ensemble using a semi-isotropic pressure coupli

[gmx-users] problem with REMD run continuation

Hi, I need to run a replica exchange md simulations of a peptide with implicit solvent and noe-distance restraints with 8 replicas and the -maxh option (the full command is mpirun -np 8 mdrun_mpi -maxh 0.5 -cpt 2 -multi 8 -replex 1000 -v -pd -s gbsa_md1_.tpr -o gbsa_md1_.trr -c gbsa_md1_.gro -e

[gmx-users] www site is temporarily down

Hi all, There was a power outage which affected the www.gromacs.org server. The system is being fixed at the moment and therefore unreachable. We expect it to be online soon though. Cheers, Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx

[gmx-users] Re: Polarizable halide (Iodide)

David, What should not be working in the current version? Do you mean that any polarizable model (water for example) can run on a single processor only? I am currently using the model by Roux et al. for NaCl solution in SWM4-NDP model and everything seems to be working fine. I also had some prob