<br><br><div class="gmail_quote">On Thu, Jun 30, 2011 at 7:57 PM, Jianguo Li <span dir="ltr"><<a href="mailto:ljggmx@yahoo.com.sg">ljggmx@yahoo.com.sg</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div><div style="font-family:times new roman,new york,times,serif;font-size:12pt">Hi Amit,<br><br>I also encountered the same problem you mentioned.<br>In v4.5, when using -nstlp wiht large value (e.g., 10000000), I got one file "localpressure.dat0". I tested first several frames of a trajectory, the calculated pressure is not the average of the pressure of individual frames. <br>
<br></div></div></blockquote><div><br></div><div>In v4.5 it outputs the profile for frames in separate files which is ok. My concern is what exactly is going in v 4.0 where there is only one file for all the frames.</div>
<div><br></div><div>Also where did you download v4.5 and v4.0 from ?</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div><div style="font-family:times new roman,new york,times,serif;font-size:12pt">
Btw, did you use CHARMM FF in your simulations and how did you convert <span style="font-family:arial, sans-serif;font-size:13px;border-collapse:collapse">the tpr files from v 4.5 to v 4.0?<br></span></div></div></blockquote>
<div><br></div><div>Yes i have used CHARMM FF and i will have to figure out the conversion. </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div><div style="font-family:times new roman,new york,times,serif;font-size:12pt">
<span style="font-family:arial, sans-serif;font-size:13px;border-collapse:collapse"><br></span><div>Cheers<br>Jianguo<br></div><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><br><div style="font-family:times new roman, new york, times, serif;font-size:12pt">
<font face="Tahoma" size="2"><div class="im"><hr size="1"><b><span style="font-weight:bold">From:</span></b> Amit Choubey <<a href="mailto:kgp.amit@gmail.com" target="_blank">kgp.amit@gmail.com</a>><br></div><b><span style="font-weight:bold">To:</span></b> Jianguo Li <<a href="mailto:ljggmx@yahoo.com.sg" target="_blank">ljggmx@yahoo.com.sg</a>>; 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, 1 July 2011 10:32:07<br><b><span style="font-weight:bold">Subject:</span></b> Re: [gmx-users] Re: local pressure v4.5 issues<br></font><div><div></div><div class="h5">
<br><span style="font-family:arial, sans-serif;font-size:13px;border-collapse:collapse">Hello Everyone,<div><br></div><div>The <span style="font-family:arial, sans-serif;font-size:13px;border-collapse:collapse"> git version of local pressure calculation at </span></div>
<div style="color:rgb(80, 0, 80)"><div><span style="font-family:arial, sans-serif;font-size:13px;border-collapse:collapse"><br></span></div><div><span style="font-family:arial, sans-serif;font-size:13px;border-collapse:collapse"><a rel="nofollow" href="http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure" style="color:rgb(0, 0, 204)" target="_blank">http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure</a></span></div>
<div><br></div></div><div>is broken. I could not get it to work for my simulations.</div><div><br></div><div>I installed gromacs local pressure version 4.0 from</div><div><br></div><div><a rel="nofollow" href="ftp://ftp.gromacs.org/pub/tmp/" style="color:rgb(0, 0, 204)" target="_blank">ftp://ftp.gromacs.org/pub/tmp/</a></div>
<div><br></div><div>I used <a rel="nofollow" href="ftp://ftp.gromacs.org/pub/tmp/gromacs-4.0.2_localpressure.tar.gz" style="color:rgb(0, 0, 204)" target="_blank">gromacs-4.0.2_localpressure.tar.gz</a> in that folder. </div>
<div><br></div>
<div>The pressure values printed using this version seem reasonable to me. I converted all the tpr files from v 4.5 to v 4.0.</div><div><br></div><div>The output of the mdrun in v 4.0 is a single file "localpressure.dat" . On the contrary in v 4.5 there were separate "localpressure.dat*" files for each frame. </div>
<div><br></div><div>I am not sure what exactly is the content of "localpressure.dat". Does it have the time averaged value of pressure tensor for each voxel ? It doesnt seem so to me because i tried it over only two frames (3 reruns were done for two frames separately and a .trr which had these two frames only) and the numbers did not seem to be averages.</div>
<div><br></div><div>Can someone help me in figuring out what is going on ?</div><div><br></div><font color="#888888"><div>Amit</div></font></span><br><div class="gmail_quote">On Tue, Jun 21, 2011 at 9:16 AM, Amit Choubey <span dir="ltr"><<a rel="nofollow" href="mailto:kgp.amit@gmail.com" target="_blank">kgp.amit@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br><br><div class="gmail_quote"><div>On Tue, Jun 21, 2011 at 1:13 AM, Jianguo Li <span dir="ltr"><<a rel="nofollow" href="mailto:ljggmx@yahoo.com.sg" target="_blank">ljggmx@yahoo.com.sg</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><div>Hi Amit,<br><br>May I ask you a question? <br>In your calculation of local pressure using a trajectory file, did you get a single averaged localpressure.dat file? Or else you get a bunch of separate files for each frame (e.g., localpressure.dat0, localpressure.dat1, localpressure.dat2 ....)?<br>
</div></div></div></blockquote><div><br></div></div><div>Yes I do get different files for different trajectories. All the files seem to have the same problem ie a very large/small number printed as tensor elements of the pressure for some of the voxels.</div>
<div><br></div><div>Do you have such problems ? Could we compare our methodologies to use the local pressure version ?</div><div><br></div><font color="#888888"><div>Amit</div></font><div><div></div><div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><div><br>Thank you very much!<br><br>Cheers,<br>Jianguo<br><br></div><div style="font-family:times new roman, new york, times, serif;font-size:12pt">
<br><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight:bold">From:</span></b> Amit Choubey <<a rel="nofollow" href="mailto:kgp.amit@gmail.com" target="_blank">kgp.amit@gmail.com</a>><br>
<b><span style="font-weight:bold">To:</span></b> Discussion list for GROMACS users <<a rel="nofollow" href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br><b><span style="font-weight:bold">Sent:</span></b> Monday, 20 June 2011 07:08:03<br>
<b><span style="font-weight:bold">Subject:</span></b> [gmx-users] Re: local pressure v4.5 issues<br></font><div><div></div><div><br>Dear all,<div><br></div><div>I did another simulation with only SPC water. Then I used the local pressure gromacs to calculate the stresses. It seems to be reasonable. </div>
<div><br></div><div>I am not sure how to figure out what goes wrong with my previous simulations when plugged into the local pressure gromacs.</div>
<div><br></div><div>Could someone help me in figuring out whats the issue ?</div><div><br></div><div>Thank You.</div><div><br><div class="gmail_quote">On Fri, Jun 17, 2011 at 6:00 PM, Amit Choubey <span dir="ltr"><<a rel="nofollow" href="mailto:kgp.amit@gmail.com" target="_blank">kgp.amit@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear all,<br><br>I installed the git version of local pressure calculation from <br><br>
<a rel="nofollow" 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>The I invoked mdrun<br>
<br>
mdrun_lp -v -s rerun.tpr -g rerun_log -olp -rerun traj0.gro -localpgrid 0.1<br><br>This created a file named "localpressure.dat0". This is a binary file so I could not look at it directly. I am not sure if there is a tool in the gromacs to look at it directly. <br>
<br>To look at the data in "localpressure.dat0" I used the planar_av.c code available in "pressure-tools" folder at<br><br><a rel="nofollow" href="http://md.chem.rug.nl/cgmartini/index.php/3d" target="_blank">http://md.chem.rug.nl/cgmartini/index.php/3d</a><br>
<br>When I look at the Pressure tensor averaged over xy plane, some of the numbers are reasonable but few of them are ridiculously large numbers which is not expected. <br><br>I checked this on two different simulations and I got the same problems. The simulations had run OK previously.<br>
<br>Could someone help me in figuring our whats going on ?<br><font color="#888888"><br>Amit Choubey<br>
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