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>
*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> <mailto: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
>
> ========================================
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-- ========================================
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
========================================
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