[Bulk] Re: [gmx-users] Re: Targeted MD

Yang Ye leafyoung at yahoo.com
Thu Jan 10 18:56:20 CET 2008

Protein are defined by the residue names inside aminoacids.dat. So, it 
is possible for nucleic acid to be "Protein".

Steven Kirk wrote:
> 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' ?
> Thanks!
> Steve Kirk

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