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!
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> To: Discussion list for GROMACS users <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
