<div><font style="BACKGROUND-COLOR: #ff0000">Thanks a lot for the detailed and nice explainations.</font></div>
<div><br><br> </div>
<div><span class="gmail_quote">2008/1/10, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>>:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">wei-xin xu wrote:<br><br>> Some hints on practices that generally *not a good idea* to use:<br>><br>
> * Do not use separate thermostats for different components of your<br>> system. Some molecular dynamics thermostats only work well in the<br>> thermodynamic limit. If you use one thermostat for, say, a small
<br>> molecule, another for protein, and another for water, you are<br>> likely introducing errors and artifacts that are hard to predict.<br>> In particular, do not couple ions in aqueous solvent differently
<br>> from that<br>> * solvent.<br>><br>> Sorry that I do not actually understand here. The link I copied above<br>> shows that better not to "couple ions in aqueous solvent differently<br>> from that solvent". Maybe not separately but differently (mean different
<br>> temperature)?<br><br>"differently" is intended to mean "in a separate group". I'll reword my<br>wiki sentence.<br><br>The original poster showed an .mdp file where<br><br>tc-grps = Protein ; SOL CL UNK
<br><br>(or something like that). Now actually, the semicolon starts a comment,<br>so he's only thermostatting the protein. That's a bad idea because it<br>will lead to net heat flow from the protein to the rest of the system.
<br>Even if there were no semicolon, there are probably a few thousand<br>solvent molecules and a handful of chloride ions. Temperature is defined<br>from the average kinetic energy, and the average kinetic energy of a<br>
handful of ions in thermal contact with many other atoms will have large<br>fluctuations, and this will lead to the thermostat doing lots of<br>corrections, for lots of heat flow in and out of the system. So treating<br>solvent+ions+other_small_stuff as one group for T-coupling purposes is a
<br>good idea, and the standard group "Non-Protein" serves well here. So a<br>usual tc-grps line has "Protein Non-Protein" for a protein simulation.<br><br>Mark<br>_______________________________________________
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