Re: [gmx-users] Possible Bug GROMACS 3.3.1 - NMA

Maik Goette wrote: Hi I just observed very strange results with my system (around 700 atoms in vacuum), when doing normal mode analysis. The eigenvalues were all negative. I then took an old nma-system from Bert de Groot and did the nma with 3.3.1 on it and observed the same strange results.

[gmx-users] missing atom in .rpb: fatal error in pdb2gmx

Dear Users, When running pdb2gmx I get this error: Program pdb2gmx, VERSION 3.3.1 Source code file: add_par.c, line: 221 Fatal error: Atom NZ1 not found in rtp database in residue LYSH, it looks a bit like NZ Dr. David van der Spoel already suggested to rename the atom in the pdb file which I

[gmx-users] radial densities

Hi guys, maybe I ask stupid question and I missed something, but I want to compute radial densities (perpendicular to an axis of a alpha helix peptide), but I couldn't find suitable program to do this job. Thanks a lot for help Milan ___ gmx-users

[gmx-users] OPLS + ffgmx

Hi all, I am trying to do a membrane protein simulation. I want to use OPLS - AA force field for protein and ffgmx (modified ffgmx force filed with lipid parameters from user contribution section ) force field for POPE lipids. Is it is possible and advisable to use two different force fields

Re: [gmx-users] OPLS + ffgmx

I posted the procedure and not the modified files mostly because this is my modification of somebody else's files. Without permission, it is not reasonable for me to redistribute them. In order to both help you and still treat the originals with due respect, I have attached snippets that will help

Re: [gmx-users] OPLS + ffgmx

Hi all, I am trying to do a membrane protein simulation. I want to use OPLS - AA force field for protein and ffgmx (modified ffgmx force filed with lipid parameters from user contribution section ) force field for POPE lipids. Is it is possible and advisable to use two different force