<br><br><div class="gmail_quote">On Wed, Sep 7, 2011 at 12:30 AM, Shou-Chuang Yang <span dir="ltr"><<a href="mailto:shcyang@ucdavis.edu">shcyang@ucdavis.edu</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 class="im">On Wed, Sep 7, 2011 at 12:11 AM, Amit Choubey <span dir="ltr"><<a 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, Sep 6, 2011 at 10:07 PM, Shou-Chuang Yang <span dir="ltr"><<a href="mailto:shcyang@ucdavis.edu" target="_blank">shcyang@ucdavis.edu</a>></span> wrote:<br></div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>
Dear gmx-users,<div><br></div><div>Could anyone help me with the calculation of 3D pressure profile in a function of y?</div><div>I used the provided gromacs-4.0.2_localpressure for my calculatioin. It calculate</div><div>
the 3D pressure profile as a function of z (the default setting of bilayer normal </div><div>is z-direction). </div><div><br></div><div>In my case, I have a bilayer which rotate at the first few nano second run</div></div>
<div>
and remained normal to y-directiona for the rest. How can I obtain a 3D pressure analysis</div><div>along the y-direction?</div></blockquote><div>Couldnt you rotate your box so that the bilayer is in z dir ?</div></div></blockquote>
<div><br></div></div><div>The local pressure analysis need to read the trajectory file with both positions and velocities. </div><div>I thought of rotate my system and rerun it for the last 600 ns ( I am using MARTINI), but since</div>
<div>I am also doing semiisotropic coupling, I cannot "rotate" the pressure coupling directions.</div><div><br></div><div>Another way I tried is to modify the output .trr into another .trr which y and z columns printed out</div>
<div>reversely as well as the Vy and Vz columns. Thinking that maybe the analysis code will read my</div><div>"originally y coordinates" as "z coordinates". What I got was segmentation fault. </div></div>
</blockquote><div><br></div><div>Why do you get a segmentation fault if you swap the y and z coordinates,velocity columns?</div><div><br></div><div>Another way around is to change the simple_localpres_analysis.c code. If you look into it there is a loop that runs over boxes in z direction to calculate pressure tensor in z direction. You could change it to y.</div>
<div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="gmail_quote"><div>
I am not sure whether it will work out eventually. </div><div class="im"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div>I really appreciated your help! </div><div><br></div><div><div>Thanks,</div><div>Joanne</div>
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</div>-- <br><span style="border-collapse:collapse;color:rgb(136, 136, 136);font-family:arial, sans-serif;font-size:13px">Shou-Chuang Yang<br>
Master’s Candidate<br>Department of Chemical Engineering and Materials Science<br>University of California, Davis<br>Phone: <a href="tel:1-646-639-4240" value="+16466394240" target="_blank">1-646-639-4240</a><br></span><br>
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