Flexibility is always desirable. For example, in free energy
calculations, sometimes one group (i.e. part of the protein, or a small
molecule) is decoupled or partly decoupled from the rest of the system.
In this case it's quite useful to be able to have a separate thermostat
for the ligand or the part of the protein, since it's not interacting
with the rest of the system (or partially noninteracting) and so there
is actually no (or little) heat transfer. Presumably there are
many other cases where you would want to do this sort of thing.<br>
<br>
David<br>
<br><br><div><span class="gmail_quote">On 2/15/06, <b class="gmail_sendername">David Mathog</b> <<a href="mailto:mathog@caltech.edu">mathog@caltech.edu</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;">
There are various predefined groups which may be specified in the<br>tc-grps parameter file field. The gmxdemo and speptide demos use<br>"Protein Sol" and the other demos use "System".<br><br>This is so not my field, but the members of the Protein and Sol
<br>groups are in intimate contact with each other so in the real world<br>all of those elements would be in thermal equilibrium with each other.<br><br>Why then use separate couplings to represent a protein system<br>in Gromacs?
<br><br>Thanks,<br><br>David Mathog<br><a href="mailto:mathog@caltech.edu">mathog@caltech.edu</a><br>Manager, Sequence Analysis Facility, Biology Division, Caltech<br>_______________________________________________<br>gmx-users mailing list
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