[gmx-users] about solvate

[Tsjerk Wassenaar]

Hi Rui Li,

That depends on the time scale...

Tsjerk

On 5/31/07, Rui Li <moonfine at mail.sdu.edu.cn> wrote:
>
> Dear Mark
>
> Thanks for your reply.
> But I think in the MD process, these original water molecules will move freely,
> even leave the active site. and the new molecules will replace them. Is it
> correct?
>
> 在您的来信中曾经提到:
> >From: Mark Abraham <Mark.Abraham at anu.edu.au>
> >Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >Subject: Re: [gmx-users] about solvate
> >Date:Thu, 31 May 2007 14:13:34 +1000
> >
> >Rui Li wrote:
> > > yes,there are some water molecules embedded in an enzyme active site.If I
> remove
> > > them,and use genbox to get new water molecules , Does it influence the
> simulation
> > > result?
> >
> > Of course! If you have any appreciation for how enzymes work, you'll
> > quickly realise that anything in the active site is finely tuned for
> > being there. If you don't know how enzymes work in general, don't
> > simulate them without reading a lot of literature on simulating enzyme
> > mechanisms.
> >
> > I cannot imagine a reason why you would want to remove such waters and
> > rely on genbox to insert a random number of water molecules depending on
> > steric clashes between arbitrarily placed atomic boundaries.
> >
> > Mark
> > _______________________________________________
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>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623