<br><br><div class="gmail_quote">On Sat, May 7, 2011 at 11:02 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im"><br>
<br>
Dimitar Pachov wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hello,<br>
<br>
I have performed simulations of protein+ligands (solute) in truncated octahedral unit cell of waters (solvent). I would like to retain the shape of unit cell and have the solute centered in such a way as to be completely surrounded by solvent. At this point, I cannot achieve this although I have exhausted my knowledge about using the trjconv options. My question is:<br>
<br>
1. How can one recenter solvent around solute and at the same time keep the original unit shape?<br>
I used the following command to get this picture:<br>
<br>
trjconv -f run.xtc -s run.tpr -n index-all.ndx -o traj/run-test.xtc -pbc mol -center -ur compact<br>
<br>
</blockquote>
<br></div>
Use -ur tric instead of -ur compact.<br></blockquote><div><br></div><div><br></div><div>This does not work. Neither is the solute always surrounded by solvent for every frame (it goes out of the box) nor is the original unit cell (truncated octahedron) preserved. </div>
<div><br></div><div>I don't understand how one can achieve this, and if there is a way to do it, why it has not been clearly explained elsewhere.</div><div><br></div><div>Thanks,</div><div>Dimitar</div><div><br></div>
<div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
-Justin<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
where for centering the solute was used and the whole system was saved to the output trajectory. <br>
Thanks,<br>
Dimitar<br>
<br>
<br>
<br>
</blockquote>
<br></div>
-- <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> | (540) 231-9080<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>
<br>
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