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 href="mailto:kgp.amit@gmail.com">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 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 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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