[gmx-users] any chance to write avoid writing out trr but only xtc file ?

Thanks Berk, I agree that a single file open action is not going to cause a lot of system activity. We're simply trying to cut down wherever possible as this is a large shared cluster where the activity of many users distributed amongst 30K cores is overwhelming the GPFS. We have been ins

RE: [gmx-users] any chance to write avoid writing out trr but only xtc file ?

for all in and output files with multiple possible file names. In git master only the master process calls fexist. Berk > Date: Wed, 2 Dec 2009 09:17:00 -0500 > From: chris.ne...@utoronto.ca > To: gmx-users@gromacs.org > Subject: [gmx-users] any chance to write avoid writing out

[gmx-users] any chance to write avoid writing out trr but only xtc file ?

We have the same desire on a large cluster in order to reduce the number of file operations overall. In addition to Xavier's suggestion, you can also write your .trr to memory: mdrun -deffnm xx -t /dev/shm/xx.trr or to the local disk: mdrun -deffnm xx -t ${TMPDIR}/xx.trr if those exist and dep

Re: [gmx-users] any chance to write avoid writing out trr but only xtc file ?

Jörn-Benjamin Lenz wrote: dear users of gromacs, i updated my gromacs from 4.0.1 to 4.0.5 and now i am facing the following problem: Good move, version 4.0.1 was badly broken :) using the older version of gromacs I submitted REMD jobs to our cluster (which also was updated from suse 10.

Re: [gmx-users] any chance to write avoid writing out trr but only xtc file ?

you can define the frequency of writing to the trr file in the mdp file. using: nstxout = 0 nstvout = 0 nstfout =0 should fix your problem. On Dec 1, 2009, at 4:30 PM, Jörn-Benjamin Lenz wrote: dear users of gromacs, i updated my gromacs from 4.0.1 to 4.0.5 and now i am facing the follow

[gmx-users] any chance to write avoid writing out trr but only xtc file ?

dear users of gromacs, i updated my gromacs from 4.0.1 to 4.0.5 and now i am facing the following problem: using the older version of gromacs I submitted REMD jobs to our cluster (which also was updated from suse 10.3 to suse 11.1) and two differently formatted output files were generated: trr