Thanks, Justin <br>I'll test your program soon.<br><br>Today also I have some problems with generation of the posre for lipids<br><br>I have lipid bilayer in pdb. Then I selected one lipid molecule and move it to separate pdb and convert it to gro via editconf.<br>
Than I've used genres and generate posre file for 1 lipid. Than I include tis posre to topology of my bilayer<br>using gropt I obtain eror that I'm using wrong posre topology<br><br>Also I've tried to include posre.itp to my lipid.itp ( this file contain link to posre on default) This run didnt produce any errors but as the result posres have not been worked ( I obtained perturbed bilayer after minimization)<br>
<br>How I can generate work posre for my bilayer to prevent perturbation after equilibration or minimization ?<br><br>James<br><br><div class="gmail_quote">2011/10/31 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im"><br>
<br>
James Starlight wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
In some papers I found Gromacs graphs showed indirectly measurements of the time evolution of the Area per lipid value. What gromac's program could be used for it for cheacking the above value during simulation runs ?<br>
<br>
</blockquote>
<br></div>
There is no Gromacs tool for this. For a simple membrane system, one can use g_energy to extract box vectors over time, which can then be divided by the number of lipids per leaflet to extract the APL. For systems with proteins embedded in membranes, it is no trivial exercise to make such measurements. We wrote a program several years ago that calculates APL for such systems:<br>
<br>
<a href="http://www.bevanlab.biochem.vt.edu/GridMAT-MD/" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/GridMAT-MD/</a><br>
<br>
The program can only be run on single snapshots at the moment, but you can assemble time evolution from the output.<div><div></div><div class="h5"><br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<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.<u></u>vt.edu/Pages/Personal/justin</a><br>
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