Dear all, Could anyone direct me to the manual for local pressure calculation or a place where everything is mentioned about it ? I have been only able to collect bits and pieces from the mailing lists.
Thank you Amit On Wed, Jun 15, 2011 at 5:35 AM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > On 15/06/2011 9:09 PM, Jianguo Li wrote: > > Dear all, > > I have made a test calculation of local pressure using version 4.5 for my > membrane simulation using CHARMM FF. When rerun the simulation, mdrun gives > the localpressure data. Howeve, instead of giving an anveraged data of the > local pressure, mdrun gives a separate file for each frame, so I got many > files: localpressure.dat0, localpressure.dat1, localpressure.dat2, > localpressure.dat3 ...... > Then I need to calculate the pressure tensor for each frame and make > average. but these localpressure.dat files are very big (each file is about > 30 Mb), occupying large space of the hard disk. Can anyone give some > suggestions on how to fix this? Thank you very much! > > > I would expect that the output frequency is configurable, but can only > suggest you consult what documentation exists for this version. Your main > alternatives are > > * to compress the files with (say) bzip2 or (less effective) gzip and > construct a script to uncompress them singly and analyse them "on the fly" > (AMBER users do a bit of this kind of thing, Google around) > * to discard ones that are too frequent. However, judging from the numbers > below, every 100ps is probably OK. > > Mark > > > The command is: > mdrun_d -s lp.tpr -rerun box_md5.trr -x box_md5_rerun.xtc -o > box_md5_rerun.trr -g md5_rerun.log -localpgrid 0.1 > And the output message is: > ........ > Dumping local pressure based on 1 frames to localpressure.dat0... > Reading frame 2 time 119400.000 > > Dumping local pressure based on 1 frames to localpressure.dat1... > Reading frame 3 time 119500.000 > > Dumping local pressure based on 1 frames to localpressure.dat2... > Reading frame 4 time 119600.000 > > Dumping local pressure based on 1 frames to localpressure.dat3... > Reading frame 5 time 119700.000 > > Dumping local pressure based on 1 frames to localpressure.dat4... > Reading frame 6 time 119800.000 > ....... > > Cheers, > Jianguo > > > > ------------------------------ > *From:* Justin A. Lemkul <jalem...@vt.edu> <jalem...@vt.edu> > *To:* Discussion list for GROMACS users > <gmx-users@gromacs.org><gmx-users@gromacs.org> > *Sent:* Friday, 10 June 2011 07:10:35 > *Subject:* Re: [gmx-users] local pressure calcuation for Gromacs-4.5 > > > > Amit Choubey wrote: > > Thanks Justin, I tried to install the recent git version but the > configure file is missing. How should I install this version ? > > > > Run the bootstrap script. It generates the configure script. > > -Justin > > > > > On Thu, Jun 9, 2011 at 12:45 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: > jalem...@vt.edu>> wrote: > > > > > > > > Amit Choubey wrote: > > > > Dear all, > > > > I saw an unanswered post at > > > http://lists.gromacs.org/pipermail/gmx-users/2011-January/058063.html > > > > It is about calculating local pressure in v 4.5 when using > > CHARMM FF. Could someone give me some pointers about this? > > > > > > I don't know what the development status of version 4.5 is, but you > > can access it at: > > > > > http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure > > > > It hasn't been merged with release-4-5-patches in some time, so many > > resolved bugs won't be fixed. > > > > -Justin > > > > -- ======================================== > > > > Justin A. Lemkul > > Ph.D. Candidate > > ICTAS Doctoral Scholar > > MILES-IGERT Trainee > > Department of Biochemistry > > Virginia Tech > > Blacksburg, VA > > jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 > > <tel:%28540%29%20231-9080> > > 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/Support/Mailing_Lists/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/Support/Mailing_Lists > > > > > > -- ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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/Support/Mailing_Lists/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/Support/Mailing_Lists > > > > -- > 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/Support/Mailing_Lists/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/Support/Mailing_Lists >
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