Hi João, I don't remember EM runs ever producing .xtc files, maybe to prevent people to use them when "grompp'ing" in the next step. (they're at much lower precision) <br><br>Anyway, that would be nice in case you want to see what's going on during EM.<br>
<br><br><div class="gmail_quote">On Fri, Jan 7, 2011 at 7:02 PM, João Rodrigues <span dir="ltr"><<a href="mailto:anaryin@gmail.com">anaryin@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hello all,<br><br>I'm trying to run energy minimization on my system (protein complex). Since it's a bit big (produces 2GB of trr files using l-bfgs) I'm trying to supress most of this output and replace the trr file with an xtc file.<br>
<br>I'm using these options in my mdp file (output related):<br><span style="font-family: courier new,monospace;"></span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">nstxout = 0</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">nstvout = 0</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">nstfout = 0</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">nstcalcenergy = 0</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">nstlog = 0 </span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">nstenergy = 0 </span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">nstxtcout = 10 </span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">xtc-precision = 1000</span><br><br>Still, I get no xtc file (even if I explicitly run mdrun with the -x option) and I still get a large trr file.<br><br>Am I doing something wrong?<br>
<br>Best!<br><font color="#888888"><br clear="all">João Rodrigues<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>Diego Enry B. Gomes<br>Laboratório de Modelagem e Dinamica Molecular<br>
Universidade Federal do Rio de Janeiro - Brasil.<br>