[gmx-users] Re: Targeted MD

Steven Kirk 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.
> 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' ?


Steve Kirk
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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