<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
Qing Zhu wrote:
<blockquote cite="mid436F924D.3010002@ttu.edu" type="cite">Hi David
<br>
<br>
I tried to run 3.2.1 tpr with 3.3 using 3 fs as the time step, but the
simulation still crashed after several thousand steps. I have no idea
why there is huge differece between 3.2.1 tpr and 3.3 tpr, because all
the initial conditions are the same except the gromacs version. Any
suggestion?
<br>
</blockquote>
decrease the time step?<br>
<blockquote cite="mid436F924D.3010002@ttu.edu" type="cite"><br>
Thanks
<br>
Qing Zhu
<br>
<br>
David wrote:
<br>
<br>
<blockquote type="cite">On Fri, 2005-11-04 at 16:01 -0600, Qing Zhu
wrote:
<br>
<br>
<br>
<blockquote type="cite">Hi David,
<br>
<br>
What I did is to run 3.2.1 tpr files with 3.2.1, and run 3.3 tpr files
with 3.3.
<br>
<br>
</blockquote>
Try 3.2.1 tpr with 3.3
<br>
<br>
<br>
<br>
<blockquote type="cite">The results of gmxcheck have hundreds of
pages, and I don't know what could I get from gmxcheck.
<br>
<br>
</blockquote>
See whether the difference is in the tpr or in mdrun.
<br>
If you have hundreds of page (pipe it through more) it may mean that
you
<br>
are using a different force field, different coordinate/velocities
which
<br>
means you can not compare the simulations.
<br>
<br>
<br>
<br>
<br>
<blockquote type="cite">Thanks
<br>
Qing Zhu
<br>
<br>
<br>
David wrote:
<br>
<br>
<br>
<blockquote type="cite">On Fri, 2005-11-04 at 15:25 -0600, Qing
Zhu wrote:
<br>
<br>
<br>
<br>
<blockquote type="cite">Hi, everyone
<br>
<br>
I tried to run lipid membrane simulations by setting the time step to
be 3 fs using gromacs-3.3, and my simulations always crashed after a
short time unless I changed the time step back to 2 fs. But if I run
the same lipid membrane simulations using gromacs-3.2.1, I can even use
4 fs as time step and the simulations runs fine. It is not a big
problem for me, but I am just curious that why gromacs-3.3 is so
critical about the time step. Any one has an idea?
<br>
<br>
<br>
</blockquote>
Did you try running your 3.2.1 tpr file with 3.3 ? Did you compare
3.2.1 and 3.3 tpr files (using gmxcheck)? <br>
<br>
<br>
<br>
<blockquote type="cite">Thanks
<br>
Qing Zhu
<br>
_______________________________________________
<br>
gmx-users mailing list
<br>
<a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
<br>
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a>
<br>
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.
<br>
<br>
<br>
</blockquote>
</blockquote>
_______________________________________________
<br>
gmx-users mailing list
<br>
<a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
<br>
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a>
<br>
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.
<br>
<br>
</blockquote>
</blockquote>
<br>
_______________________________________________
<br>
gmx-users mailing list
<br>
<a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
<br>
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a>
<br>
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.
<br>
<br>
</blockquote>
<br>
<div class="moz-signature">-- <br>
<i>Regards,</i><br>
Yang Ye<br>
<small><i>Computational Biology Lab<br>
School of Biological Sciences<br>
Nanyang Technological University<br>
Singapore<br>
Tel: 6316-2884<br>
</i></small>
</div>
</body>
</html>