Thanks Tsjerk,<br><br>I am rerunning the simulation with SDS+SOL+IONS in a single tcoupl group. <br>I was trying to anneal because, I suspected huge velocities on the atoms due to a "high starting temperature", well not high enough to be worried and I had done a NVT equilibration already, so shouldn't cause any problems, but I just wanted to be sure.
<br>I am running the SDS simulations with water simultaneously... haven't checked its properties yet. <br><br>Venky<br><br><div><span class="gmail_quote">On 4/25/07, <b class="gmail_sendername">Tsjerk Wassenaar</b> <
<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi Venky,<br><br>On 4/25/07, Venky Krishna <
<a href="mailto:venky.agas@gmail.com">venky.agas@gmail.com</a>> wrote:<br>> Hi gmx-users,<br>><br>> System Setup:<br><br>Looks good<br><br>><br>> Problem:<br><br>Did you check the PRODRG2 derived parameters? Run through the molecule
<br>yourself (draw it!). Check the atom, bond, etc. types. Also, run a<br>simulation of only SDS (with water) to check the properties, like the<br>area per lipid, etc.<br><br>><br>> Parameters:<br><br>Won't go through all this... (but thanks for adding it..., makes it a
<br>good mail..., I'm just being lazy).<br><br>> and here are my relevant MD mdp parameters.<br><br>> tc-grps = Protein SDS SOL Na+ Cl-<br>> tau-t = 0.5
0.5 0.5 0.5 0.5<br>> ref-t = 300 300 300 300 300<br><br>This is BAD BAD BAD! We just dealt with this issue a few times in the<br>past few weeks! It may be the cause of your problem, and you should
<br>fix it and rerun the simulation, before turning back to the list.<br>Merge your sodium and chloride with the solvent, so you have three<br>reasonably large groups to couple to the heat bath. Check the archives<br>on this one.
<br><br>> ; SIMULATED ANNEALING<br>> ; Type of annealing for each temperature group (no/single/periodic)<br>> annealing = single single single single single<br>> ; Number of time points to use for specifying annealing in each group
<br>> annealing_npoints = 2 2 2 2 2<br>> ; List of times at the annealing points for each group<br>> annealing_time = 0 20 0 20 0 20 0 20 0 20<br>> ; Temp. at each annealing point, for each group.
<br>> annealing_temp = 0 300 0 300 0 300 0 300 0 300<br><br>Is there any specific reason for annealing here? You didn't mention it<br>in your setup.<br><br>Cheers,<br><br>Tsjerk<br><br>--<br>Tsjerk A. Wassenaar,
Ph.D.<br>Junior UD (post-doc)<br>Biomolecular NMR, Bijvoet Center<br>Utrecht University<br>Padualaan 8<br>3584 CH Utrecht<br>The Netherlands<br>P: +31-30-2539931<br>F: +31-30-2537623<br>_______________________________________________
<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at
<a href="http://www.gromacs.org/search">http://www.gromacs.org/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/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></div><br><br clear="all"><br>-- <br>Venks
<br><br>~ You will become rich and famous, unless you don't.