[gmx-users] Re: problems with reaction field (Anton Feenstra)

[Anton Feenstra]

Alan Wilter Sousa da Silva wrote:
> On Wed, 24 Sep 2003 gmx-users-request at gromacs.org wrote:
> 
> 
>>   3. Re: problems with reaction field (Anton Feenstra)
> 
> 
> Date: Mon, 22 Sep 2003 19:05:43 +0200
> From: Anton Feenstra <feenstra at chem.vu.nl>
> To:  gmx-users at gromacs.org
> Subject: Re: [gmx-users] problems with reaction field
> Reply-To: gmx-users at gromacs.org
> 
> 
> 
>>Also, I noticed you use separate t-coupling for solvent, ions,
>>protein and ligand, which I could guess may give artefacts in
>>combination with cut-offs?
> 
> 
> Hi, now I got confused.  Separated t-coupling is not the better choice in 
> any case?  Which sort of artefacts?

OK, I'm not the expert on this, and it will probably be dependent on the
system you're simulating, but I always couple two separate groups, one
for Protein + co-factors + ligands, and one for water + ions. There may
be artefacts in coupling groups with few atoms, but as well there may be
artefacts in coupling a (large) group in which some atom(s) do not exchange
heat well with the rest of the group.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
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