[gmx-users] Addition of ions in vacuum simulations

Xavier Periole X.Periole at rug.nl
Thu Oct 18 09:23:50 CEST 2007

What Mark means is that there us little meaning of adding ions in
a simulation of a protein in vacuum.

There is little sense and use of a simulation of a protein in vacuum,
but that could depend on what you are looking for.

There is little sense in putting ions in a vacuum environment to
neutralize your system, this does not depend on your problem.

The other option you have to neutralize the system is to neutralize
the side-chains so that here is no more net charges in your system.

This what is done in a Gromos FF version. check in the pdb2gmx options.


>> I think, it is not a chemistry question exactly.
>> Genion command asks for a group whose atoms are replaced with ions.
>> I have no solvent molecules in my system.
>> In this respect, how can I incorporate ions into my system?
> Check your assumptions. Does it make sense to put isolated ions outside a
> protein in vacuum?
> 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

XAvier Periole - PhD

1- Institute of Molecular Assemblies
      City University of New York - USA
2- Molecular Dynamics-Group
      University of Groningen - The Netherlands

More information about the gromacs.org_gmx-users mailing list