Dear all,<div><br></div><div>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.</div>
<div><br></div><div>Thank you</div><div>Amit<br><br><div class="gmail_quote">On Wed, Jun 15, 2011 at 5:35 AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div text="#000000" bgcolor="#ffffff"><div class="im">
On 15/06/2011 9:09 PM, Jianguo Li wrote:
<blockquote type="cite">
<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>
</div>
</div>
</blockquote>
<br></div>
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 <br>
<br>
* 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)<br>
* to discard ones that are too frequent. However, judging from the
numbers below, every 100ps is probably OK.<br><font color="#888888">
<br>
Mark</font><div><div></div><div class="h5"><br>
<br>
<blockquote type="cite">
<div style="font-family:times new roman,new york,times,serif;font-size:12pt">
<div>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 <a href="mailto:jalemkul@vt.edu" target="_blank"><jalemkul@vt.edu></a><br>
<b><span style="font-weight:bold">To:</span></b>
Discussion list for GROMACS users
<a href="mailto:gmx-users@gromacs.org" target="_blank"><gmx-users@gromacs.org></a><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 href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">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]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>>
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-- ========================================<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]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><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>
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