[gmx-users] local pressure calcuation for Gromacs-4.5

[Jianguo Li]

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 <jalemkul at vt.edu>
To: Discussion list for GROMACS users <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>> 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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