Amit Choubey wrote:
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.
That's probably all there is to be found. There's no manual linked from the git
web interface or the ftp site.
-Justin
Thank you
Amit
On Wed, Jun 15, 2011 at 5:35 AM, Mark Abraham <mark.abra...@anu.edu.au
<mailto: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> <mailto:jalem...@vt.edu>
*To:* Discussion list for GROMACS users <gmx-users@gromacs.org>
<mailto: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> <http://vt.edu> | (540)
231-9080 <tel:%28540%29%20231-9080>
> <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 <http://vt.edu> | (540) 231-9080
<tel:%28540%29%20231-9080>
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
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Ph.D. Candidate
ICTAS Doctoral Scholar
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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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