Thanks a lot for the detailed and nice explainations.
2008/1/10, Mark Abraham <[EMAIL PROTECTED]>: > > wei-xin xu wrote: > > > Some hints on practices that generally *not a good idea* to use: > > > > * Do not use separate thermostats for different components of your > > system. Some molecular dynamics thermostats only work well in the > > thermodynamic limit. If you use one thermostat for, say, a small > > molecule, another for protein, and another for water, you are > > likely introducing errors and artifacts that are hard to predict. > > In particular, do not couple ions in aqueous solvent differently > > from that > > * solvent. > > > > Sorry that I do not actually understand here. The link I copied above > > shows that better not to "couple ions in aqueous solvent differently > > from that solvent". Maybe not separately but differently (mean different > > temperature)? > > "differently" is intended to mean "in a separate group". I'll reword my > wiki sentence. > > The original poster showed an .mdp file where > > tc-grps = Protein ; SOL CL UNK > > (or something like that). Now actually, the semicolon starts a comment, > so he's only thermostatting the protein. That's a bad idea because it > will lead to net heat flow from the protein to the rest of the system. > Even if there were no semicolon, there are probably a few thousand > solvent molecules and a handful of chloride ions. Temperature is defined > from the average kinetic energy, and the average kinetic energy of a > handful of ions in thermal contact with many other atoms will have large > fluctuations, and this will lead to the thermostat doing lots of > corrections, for lots of heat flow in and out of the system. So treating > solvent+ions+other_small_stuff as one group for T-coupling purposes is a > good idea, and the standard group "Non-Protein" serves well here. So a > usual tc-grps line has "Protein Non-Protein" for a protein simulation. > > Mark > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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