[gmx-users] Re: gmx-users Digest, Vol 58, Issue 61

Re Benchmarks, Fixed! After making all the changes that Justin suggested the dynamics run as expected, if anyone wants the scripts to run the exact same system then I am happy to send them on. Bryn ___ gmx-users mailing listgmx-users@gromacs.org ht

[gmx-users] Re: gmx-users Digest, Vol 58, Issue 59

> Robert Fenwick wrote: >> Hi, >> >> I wanted to run one of the gromacs 4.0 benchmarks on a new cluster >> that we have and also wanted to see the affect of this 4 fs time step. >> If it would not be too much trouble would it be possible for the >> setups of

[gmx-users] Gromacs 4.0 Benchmarks

Hi, I wanted to run one of the gromacs 4.0 benchmarks on a new cluster that we have and also wanted to see the affect of this 4 fs time step. If it would not be too much trouble would it be possible for the setups of either the PLINCS paper or the GROMACS 4.0 paper to be placed somewhere on the we

[gmx-users] energy and coordinates at different times

Dear All, I am starting some simulations and would like to write out some coordinates more frequently than others, is this currently possible. Below is how I envisaged using the commands, however it seems that I don't quite understand. Is something like this possible and how do I implement this?

[gmx-users] Water molecule can not be settled

Hi, My simulation has fall over with this error: t = 501.346 ps: Water molecule starting at atom 8367 can not be settled. Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates What can I do to fix it? There are a few other that have had this

[gmx-users] normal mode analysis

Hi, I am interested in comparing the normal modes of a protein with and without a ligand. I have already computed the lowest 100 normal modes for the protein (eigenvec_a.trr) and the protein:ligand complex and have reduced the protein:ligand eigenvec_b.trr to the protein by issuing; >

[gmx-users] GTP topology

Here are the topology file lines that I have added to my version of ffG43a1.rtp It should just work if you add these lines to this file. If anyone has any comments then I would be happy to have them, this is the first time I have done this. Bryn [ GTP ] [ atoms ] GN9NR-0.

[gmx-users] GTP topology file for ffG43a1

Dear all, I have now prepared what I think are the necessary lines for entry into the ffG43a1.rtp file for GTP, however I was wanting a quick way to test what I have done. Again I am open to suggestions. Specifically I want to ensure that I have added sufficient bonds and angles for the

[gmx-users] ATP, GTP and REX

Hi, I would like to make some unrestrained simulations of ATP and GTP binding proteins and wondered if there were any topology files floating about for OPLSAA or the GROMOS96.1 forcefields for these two ligands? I understand that the gmx forcefields have been deprecated and that I sho