Mark Abraham <[EMAIL PROTECTED]> wrote
Subject: Re: [gmx-users] Re: Targeted MD
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[EMAIL PROTECTED]>
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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
A supplementary question.
The tc-grps line can take predefined standard group names such as
'System', 'Protein' and 'Non-Protein'.
Does the 'Protein' group need to actually BE a protein, or are 'Protein'
and 'Non-Protein' really synonyms for
'PresumablyBigMoleculeOfInterestProteinOrNot' and 'EverythingElse' ?
Thanks!
Steve Kirk
--
Dr. Steven R. Kirk <[EMAIL PROTECTED], [EMAIL PROTECTED]>
Dept. of Technology, Mathematics & Computer Science (P)+46 520 223215
University West (F)+46 520 223299
P.O. Box 957 Trollhattan 461 29 SWEDEN http://beacon.webhop.org
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