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

Ran Friedman, Biochemisches Inst. r.friedman at bioc.uzh.ch
Sat Nov 24 19:20:25 CET 2007


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 

I assume you have a good reason to simulate in vacuo - the mailing list 
archives give many reasons why it's not advised.


On Sat, 24 Nov 2007 19:47:43 +0200
> 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 
> 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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