Hi, On Wed, Jul 22, 2009 at 1:13 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > Jamie Seyed wrote: > >> Thank you Justin, >> But how I can prevent from that (filesystem blip) to happen. Also May I >> > > I know nothing about your filesystem, but sometimes these things happen > randomly. Try re-running with nstxout at some value other than zero and see > if you get a non-empty .trr file. Yes, It is ok now. I re-run it with nonzero nstxout ! Thanks for all comments. > change Pcoupl= Parrinello-rahman instead of berendsen (has it any >> effect?? since I have changed Tcoupl=v-rescale instead of berendsen)? >> > > Haphazardly changing algorithms for T- and P-coupling without knowing why > is a recipe for disaster. Read the literature about each methodology, and > choose the one that's appropriate. > > The "problem" regarding box dimensions you pointed out before is related to > the fact that you are using isotropic pressure coupling, wherein the box > dimensions scale uniformly. That will be the case regardless of which > algorithm you use. If the box dimensions change, that's just reality :) > > If for some reason you want to fix the box dimensions, use Pcoupl = no. > > 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.......?? >> >> > > The .mdp file was generated using an old version of Gromacs. Refer to the > manual for changes, and delete that line from the .mdp file. > > -Justin > > Thanks, >> Jamie >> >> On Wed, Jul 22, 2009 at 11:53 AM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> 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 >> <jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> 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 gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org>> >> >> 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 gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>. >> >> 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/> <http://vt.edu/> | (540) >> 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>> >> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/searchbefore >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www >> interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>. >> >> 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 gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> 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 gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> 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 gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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