[gmx-users] about solvate

[Tsjerk Wassenaar]

Hi Rui Li,

Everything you do influences the simulation results. Whether the
results are useful depends on the question.

Cheers,

Tsjerk

On 5/31/07, Rui Li <moonfine at mail.sdu.edu.cn> 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?
>
>
> 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 00:16:37 +1000
> >
> >Rui Li wrote:
> > > Dear gmx-users:
> > >
> > > I get a pdb file,and there are some water moleculers included in it.
> > >  Should I remove these water moleculers before I use genbox?
> >
> > Depends what those waters are doing. Waters embedded in an enzyme active
> > site should probably stay... but of course with such a system you would
> > have thought about the kind of thing you wanted to study before this,
> > right? :-) Waters in crystal packing sites can probably go or stay.
> >
> > What's the problem here?
> >
> > Mark
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
>
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>


-- 
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