Thank you Justin, But how I can prevent from that (filesystem blip) to happen. Also May I change Pcoupl= Parrinello-rahman instead of berendsen (has it any effect?? since I have changed Tcoupl=v-rescale instead of berendsen)? By the way there was a warning after doing grompp, it said "unknown or double left-hand 'bd-temp' in parameter file" In file.mdp it is bd-temp=300 What about this warning related to the problem.......??
Thanks, Jamie On Wed, Jul 22, 2009 at 11:53 AM, Justin A. Lemkul <[email protected]> wrote: > > > Jamie Seyed wrote: > >> Hi Justin, >> nstxout=0 >> nstvout=0 >> >> > > Right, then the .trr file should be empty until the very end, when the last > frame should be written. Like I said, probably a filesystem blip. > > Pcoupl=berendsen >> Pcoupltype=isotropic >> >> > > Note that all of your box vectors are the same at the end. This is > probably a consequence of isotropic pressure coupling. > > -Justin > > 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]<mailto: >> [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] >> <mailto:[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] >> <mailto:[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 <http://vt.edu/> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> _______________________________________________ >> gmx-users mailing list [email protected] >> <mailto:[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] >> <mailto:[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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