Thanks a lot Tsjerk !<br>I joined SOL and Cl into one index group and removed Protein and SOLCL (the new one with SOL and CL) from energy monitoring list. It works now. i got the energy of a particular residue.<br><br>thanks for the help.
<br>kota.<br><br><div><span class="gmail_quote">On 5/1/07, <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 Kota,<br><br>So in your case, the solution is to make an index group<br>Protein_not_met1 or something like that. Note that you can always get<br>information about energies and energy contributions by using mdrun<br>-rerun and feeding a trajectory.
<br><br>Now there's one other thing:<br><br>> ; Berendsen temperature coupling is on in two groups<br>> Tcoupl = berendsen<br>> tc-grps = Protein SOL Cl<br>> tau_t =
0.1 0.1 0.1<br>> ref_t = 300 300 300<br><br>This is bad! Check the archives on temperature coupling groups (hint:<br>check last weeks archive), and think a bit about heat-baths.<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>
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