<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt"><div>Dear all,<br><br>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 ...... <br>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!<br><br>The command is: <br>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<br>And the output message is:<br>........<br>Dumping local pressure based on 1 frames to localpressure.dat0...<br>Reading frame 2 time 119400.000 <br><br>Dumping local pressure based on 1 frames to localpressure.dat1...<br>Reading frame 3 time 119500.000 <br><br>Dumping local pressure based on 1 frames to localpressure.dat2...<br>Reading frame 4 time 119600.000 <br><br>Dumping local pressure based on 1 frames to localpressure.dat3...<br>Reading frame 5
time 119700.000 <br><br>Dumping local pressure based on 1 frames to localpressure.dat4...<br>Reading frame 6 time 119800.000 <br>.......<br><br>Cheers,<br>Jianguo<br></div><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><br><br><br><div style="font-family:arial, helvetica, sans-serif;font-size:13px"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Justin A. Lemkul <jalemkul@vt.edu><br><b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Friday, 10 June 2011 07:10:35<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] local pressure calcuation for Gromacs-4.5<br></font><br><br><br>Amit Choubey wrote:<br>> Thanks Justin, I tried to install the recent git version but the
configure file is missing. How should I install this version ?<br>> <br><br>Run the bootstrap script. It generates the configure script.<br><br>-Justin<br><br>> <br>> On Thu, Jun 9, 2011 at 12:45 PM, Justin A. Lemkul <<a ymailto="mailto:jalemkul@vt.edu" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a> <mailto:<a ymailto="mailto:jalemkul@vt.edu" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>>> wrote:<br>> <br>> <br>> <br>> Amit Choubey wrote:<br>> <br>> Dear all,<br>> <br>> I saw an unanswered post at<br>> <a href="http://lists.gromacs.org/pipermail/gmx-users/2011-January/058063.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2011-January/058063.html</a><br>> <br>> It is about calculating local pressure in v 4.5 when using<br>>
CHARMM FF. Could someone give me some pointers about this?<br>> <br>> <br>> I don't know what the development status of version 4.5 is, but you<br>> can access it at:<br>> <br>> <a href="http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure" target="_blank">http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure</a><br>> <br>> It hasn't been merged with release-4-5-patches in some time, so many<br>> resolved bugs won't be fixed.<br>> <br>> -Justin<br>> <br>> -- ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> MILES-IGERT Trainee<br>> Department of Biochemistry<br>>
Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<br>> <tel:%28540%29%20231-9080><br>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>> <br>> ========================================<br>> -- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>>
Please search the archive at<br>> <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>> Please don't post (un)subscribe requests to the list. Use the www<br>> interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br>> <mailto:<a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>.<br>> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>> <br>> <br><br>-- ========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of
Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]vt.edu | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br>-- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org"
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