[gmx-users] Error while running gromacs in parellel

2008-08-22 Thread vivek sharma
Hi There, I am running gromacs in parellel using mpirun (using submit option). While doing so output file gave me error as follow srun: error: n826: task32: Terminated srun: Terminating job srun: error: n827: task40: Segmentation fault I am running gromacs for the first time (in parellel). Does

Re: [gmx-users] Help - No default Bond types dna

2008-08-22 Thread Justin A. Lemkul
Ragnarok sdf wrote: Hello. Ie been trying to run a DNA simulation with gromacs using amber99 force field. I've started with my DNA sequence complexed with the protein, but then decided to separate them to know exactly what the problem was. Now I am not even using the DNA sequence from my pdb

[gmx-users] groups to write to trr

2008-08-22 Thread Vitaly Chaban
Hi, Is it possible to write only the specified groups to the TRR trajectory like using xtc-grps key for XTC? We calculate VACFs and so need velocities to be written but only the velocity of some groups are of interest, not of all the particles. The "full" TRRs take extremely huge space... Thank