Justin,I have a question. If we download files from Peter Tieleman's website, all you get are .gro files, and no cpt files. Then what should one do? Continue using the velocities in the .gro file?<br><br><div class="gmail_quote">
On Fri, Apr 13, 2012 at 5:28 PM, 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">
<br>
<br>
James Starlight wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Gromacs Users!<br>
<br>
<br>
I want to perform simulation of the pure bilayer surrounded by water. I'm using already pre-equilibrated bilayers as the initial structure. During conversion pdb-> gro -> pdb the velocities from initial equilibration runs of the structure were lost. Should I start generating <br>
</blockquote>
<br>
Relying on a .gro file to maintain velocities is a bad idea. The values contained therein lack sufficient precision to be reliable. You should be using .cpt files to continue runs to preserve the previous ensemble, thus making the choice of coordinate file format irrelevant.<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
this velocities in my production run ( gen_Vel= yes) or i must do equilibration instead first to generate velocities? Finally what length <br>
</blockquote>
<br>
A production run should not start with newly generated velocities. Doing so destroys the initial equilibration, and if you haven't taken care to preserve that anyway, you should probably just start over and make proper use of .cpt files.<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
should this equilibration be to provide reasonable velocities for futrher MD run if I would avoild long equilibration period because of suitability of my initial model?<br>
<br>
</blockquote>
<br>
There is no universal answer to this question. It depends on your criteria for convergence and contents of the system, among other considerations.<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>
<br>
==============================<u></u>==========<span class="HOEnZb"><font color="#888888"><br>
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/<u></u>mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists</a><br>
</font></span></blockquote></div><br><br clear="all"><div><br></div>-- <br>Rajat Desikan (Ph.D Scholar)<br>Prof. K. Ganapathy Ayappa's Lab (no 13),<br>Dept. of Chemical Engineering,<br>Indian Institute of Science, Bangalore<br>