[gmx-users] Neutralizing the total charge of the system in vacuum

[David van der Spoel]

Ran Friedman, Biochemisches Inst. wrote:
> Hello,
> 
> You can add a few ions manually or use genbox. However, it's probably 
> better to use a vacuum force field and have your peptide uncharged for 
> vacuum simulations. Any ions you add will have a very strong interaction 
> with the peptide.
> 
> I assume you have a good reason to simulate in vacuo - the mailing list 
> archives give many reasons why it's not advised.
> 
It is not advised as a model for peptides in solution, but if you want 
to model something in vacuo then it is fine. In that case you may want 
to look for evidence of the charge of the peptide in vacuo from mass 
spec experiments.
> Ran.
> 
> On Sat, 24 Nov 2007 19:47:43 +0200
>  "OZGE ENGIN" <OZENGIN at KU.EDU.TR> wrote:
>> Hi all,
>>
>> I am performing a simulation in vacuum. The peptide has  nonzero 
>> charge, so I attempted to neutralize the total charge via 
>> genion;however as it is known, it asks for a continuous group for 
>> replacing, but I have no solvent molecules for the replacement.
>>
>> How can I neutralize the total charge while performing simulations in 
>> vacuum?
>>
>> Thanks in advance
>>
>> Oz.
>>
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> 
> ------------------------------------------------------
> Ran Friedman
> Postdoctoral Fellow
> Computational Structural Biology Group (A. Caflisch)
> Institute of Biochemistry
> University of Zurich
> Winterthurerstrasse 190
> CH-8057 Zurich, Switzerland
> Tel. +41-44-6354493
> Skype: ran.friedman
> ------------------------------------------------------
> 
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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://folding.bmc.uu.se
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