Hi,<div><br></div><div>are you running in parallel (either MPI or threads)? Load-balancing is one reason for different rounding errors.</div><div>You can run with "mdrun -reprod" to avoid any different rounding between runs and should in general get the same then.</div>
<div><br></div><div>Roland<br><br><div class="gmail_quote">On Fri, Jan 28, 2011 at 6:17 PM, Matthew Chan <span dir="ltr"><<a href="mailto:mchan3@connect.carleton.ca">mchan3@connect.carleton.ca</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Hi,<br><br>My second question is about the divergent energy minimization results which I have been receiving.<br><br>
I've taken the 1AKI lysozyme and prepared a single em.tpr file (1AKI is in vacuum). Afterwards I make 10 copies of the em.tpr file and use mdrun on each one. If I set the stopping condition to less than 1000kJ/mol nm, my potential energies and final structures from each run are not identical. <br>
<br>I've tried both steepest descent and cg methods for minimization. I've also checked that the Fmax is indeed less than my stopping condition, and the potential energy is negative. Is this problem well documented or is there something wrong with my system? There seem to be a few parts of the manual that allude to the possibility of variance between subsequent runs of EM. <br>
<br>If this is a well documented problem, can someone try explaining the cause to me please? I would like to learn more about this topic.<br><br>Also, the potential energy value reported seems to be several orders of magnitude different from what other programs are reporting (24 000 vs 500). What units are it expressed in?<br>
<br>Thanks in advance for your replies,<br><br>-- <br>____________<br><font color="#888888"><br>Matthew Chan<br><br>
</font><br>--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/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/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">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/Support/Mailing_Lists</a><br></blockquote></div><br><br clear="all"><br>-- <br>ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov">cmb.ornl.gov</a><br>
865-241-1537, ORNL PO BOX 2008 MS6309<br>
</div>