[gmx-users] charge on protein

[David]

On Mon, 2005-01-24 at 10:59 -0800, Gia Maisuradze wrote:
> Hi,
> 
> I also have non-zero charge in my calculations, but it is much less 
> than -15.000e, it is 1.000e or 2.000e. Is it reasonable to simulate protein 
> with this charges?
If you are able to simulate long enough it is best to add counter-ions
and use PME. 
> 
> Thanks,
> 
> Gia Maisuradze
> 
> ----- Original Message ----- 
> From: "David van der Spoel" <spoel at xray.bmc.uu.se>
> To: "4tejender" <4tejender at indiatimes.com>; "Discussion list for GROMACS 
> users" <gmx-users at gromacs.org>
> Sent: Sunday, January 23, 2005 8:32 AM
> Subject: Re: [gmx-users] charge on protein
> 
> 
> > On Sun, 2005-01-23 at 21:29 +0530, 4tejender wrote:
> >> hello users
> >>  i m new to gromacs can anyone tell me it is advisable to simulate 
> >> protein with high charge.does it effect reliablity of the dyanamics. if 
> >> yes what is a proper method to reduce the charge. i m getting waring for 
> >> a non zero charge of -15.000e during processing protein file.
> >
> > that is quite a lot. If you don't add ions it may even unfold due to the
> > charge. Be careful with a long equilibration of the solvent and ions
> > (e.g. run 2-5 ns with position restraints on the protein).
> >>
> >> thanks in advance
> >> teje
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> > -- 
> > David.
> > ________________________________________________________________________
> > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596,          75124 Uppsala, Sweden
> > phone:  46 18 471 4205          fax: 46 18 511 755
> > spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> >
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> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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