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 <[EMAIL PROTECTED]> wrote
Subject: Re: [gmx-users] Re: Targeted MD
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[EMAIL PROTECTED]>
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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