[gmx-users] about solvate

Rui Li moonfine at mail.sdu.edu.cn
Thu May 31 09:23:36 CEST 2007

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

>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
> > them,and use genbox to get new water molecules , Does it influence the
> > 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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