[gmx-users] Re: Targeted MD
Steven.Kirk at hv.se
Thu Jan 10 14:16:13 CET 2008
Mark Abraham <Mark.Abraham at anu.edu.au> wrote
> Subject: Re: [gmx-users] Re: Targeted MD
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4785945A.5070006 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 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.
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' ?
Dr. Steven R. Kirk <steven.kirk at hv.se, S.R.Kirk at physics.org>
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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