Re: [gmx-users] Invalid order for directive atomtypes

Hi Jonathan, The itp's for the ligands were given atomtype sections, but atomtypes (and other *types) may only be defined before any moleculetype definition (check chapter 5 of the manual for the topology format). You'll need to remove anything before the moleculetype directive from the itp files

[gmx-users] Re: energy conservation / frozen atoms

> On 8/2/13 3:19 PM, S. Alireza Bagherzadeh wrote: > > Thanks for your notes. > > > > > > I did a diagnosis test which could be of relevance here. > > > > I set up the following system: > > [ gas | liquid water (solid water) liquid water | gas ] > > > > gas is united atom methane. > > liquid water

[gmx-users] Re: Mean Square Displacement: gromacs 4.5 Vs gromacs 4.6.1

Hi, I effectively refer to the MSD of the protein. My simulation is different compared to the simulation of a lipid bilayer and the "normal" MSD for a protein in water should be equivalent to the red plot. I forgot to mention but the MSD are obtained from 10 ns NVE simulations. Regards, Guill

[gmx-users] REMD run on higher nodes.

Greetings I'm running REMD of 96 replicas where the run.pbs is the following: #!/bin/tcsh #PBS -S /bin/tcsh #PBS -l walltime=00:15:00 #PBS -q workq #PBS -l select=8:ncpus=12:mpiprocs=12 #PBS -l place=scatter:excl #PBS -V # Go to the directory from which you submitted the job cd $PBS_O_WORKDIR se

[gmx-users] g_wham error analysis hangs

Hi, I have a problem with the error analysis of g_wham. The PMF profile and sampling windows looks good, but when I try to generate error bars g_wham hangs. This is what I do: g_wham_mpi -if pullf-files.dat -it tpr-files.dat -o -hist -nBootstrap 50 -bins 50 -bs-method traj-gauss -bsres -ac y