Hi Justin, nstxout=0 nstvout=0 Pcoupl=berendsen Pcoupltype=isotropic
In fact I used the mdp file of /tuto/water and I modified it for PME and v-rescale. But the rest is the same (I am using version 4.0.5) I finished the simulation but I saw file.trr is empty... the rest seems fine...even file.xtc Thank you, Jamie On Wed, Jul 22, 2009 at 11:32 AM, Justin A. Lemkul <[email protected]> wrote: > > > Jamie Seyed wrote: > >> Dear all, >> I did a simulation of spce water and every thing seemed ok, when I did >> mdrun -s file.tpr -o file.trr -c file_out.gro -v -g file.log, I got a >> file.trr with zero size, but I have file.xtc that seems fine with VMD. I >> don't what happened here. Any idea? >> > > What did you set as nstxout and nstvout? Depending on what you set for > these parameters, you may not get much in the .trr file; the final frame > should have been written, however. Maybe something went wrong with the > filesystem (a blip), and the output was suppressed. I've had that happen > when a simulation is finishing and a .gro file is written, but has nothing > in it. > > Also I looked at the box size from first file.gro and last >> file_out.gro..... It shows the box size has been changed a little bit: >> first it was 1.86206 1.86206 1.86206 >> finally it is 1.86586 1.86586 1.86586 >> >> > > What kind of pressure coupling are you using (if any)? > > Can someone please kindly make it clear to me why it happened? >> >> > > In general, posting the text of your .mdp file is a good idea. That way, > the answers to my questions above are answered :) > > -Justin > > Thanks, >> Jamie >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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