[gmx-users] charge on protein
gia at chem.unr.edu
Mon Jan 24 19:59:49 CET 2005
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?
----- 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
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> 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
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