[gmx-users] g_nmtraj -temp

Dear gromacs users, g_nmtraj states that "to make the motion clearly visible in PyMol you might want to amplify it by setting an unrealistically high temperature". What temperature values do you usually need to use? To see nice domain movements, I need to set the temperature in the range 10-

RE: [gmx-users] eigenvectors with nan values

-users] eigenvectors with nan values On 20/08/2012 4:34 AM, Joaquim Rui de Castro Rodrigues wrote: > Dear Gromacs users, > > I'm having problems with g_covar because sometimes it produces eigenvectors > with nan values. This is related with a previous post > (http://lists.groma

[gmx-users] eigenvectors with nan values

Dear Gromacs users, I'm having problems with g_covar because sometimes it produces eigenvectors with nan values. This is related with a previous post (http://lists.gromacs.org/pipermail/gmx-users/2012-July/073492.html). I checked the integrity of my xtc and tpr/pdb input files, and everything se

RE: [gmx-users] 2 chain protein and VMD

Hi, You could do something like this: set sel1 [atomselect top "residue 0 to 499"] $sel1 set chain A set sel2 [atomselect top "residue 500 to 999"] $sel2 set chain B Hope this helps, Rui Rodrigues De: gmx-users-boun...@gromacs.org [gmx-users-boun...@gro

RE: [gmx-users] nan in g_anaeig -over

2012 16:48 Para: Discussion list for GROMACS users Assunto: Re: [gmx-users] nan in g_anaeig -over On 27/07/2012 12:31 AM, Joaquim Rui de Castro Rodrigues wrote: > Dear all, > > I am getting a nan while calculating the overlap between covariance matrices > (in this case, using the same vectors for

[gmx-users] nan in g_anaeig -over

Dear all, I am getting a nan while calculating the overlap between covariance matrices (in this case, using the same vectors for -v and -v2): g_anaeig455 -v atp/eigenvectors.trr -v2 atp/eigenvectors.trr -over overlap_atp-atp I tried different gromacs versions, different -last values, and als

[gmx-users] Orders of the residues in gromacs

Hi, You are probably mixing "resid" and "residue". In VMD, - "resid" is taken as found in the file (pdb, gro, etc). You may have several residues with the same "resid" if you load a file with multiple chains. - "residue" is generated internally by VMD, it is incremented by one unit for each r