[gmx-users] local pressure calcuation for Gromacs-4.5
Justin A. Lemkul
jalemkul at vt.edu
Wed Jun 15 23:17:53 CEST 2011
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.Abraham at anu.edu.au
> <mailto:Mark.Abraham at 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 <jalemkul at vt.edu> <mailto:jalemkul at vt.edu>
>> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
>> <mailto:gmx-users at 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
>> <jalemkul at vt.edu <mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu
>> <mailto:jalemkul at 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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--
========================================
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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