[gmx-users] Re: genion

Justin Lemkul jalemkul at vt.edu
Tue Feb 26 15:30:18 CET 2013

For the fourth time in two days, I'll start with:

Please keep all Gromacs-related correspondence on the gmx-users list.  I am not 
a private tutor.  I am CC'ing the list and ask that further comments and 
questions be posted there.

On 2/26/13 9:03 AM, Samadashvili Nino wrote:
> Dear Justin,
>   I am trying to add ions to my system using genion. Firstly, I define separate groups in my index file because I'd like Na and Cl mostly concentrated at the surface. However, genion does not allow me to choose the surface group (just the system / water groups are listed). Could you please help me with this problem?

It's not straightforward, but it's certainly possible.  Your index group will 
contain specific water molecules, and so those water molecules must appear as 
their own group listed in the [molecules] directive.  That requires a unique 
[moleculetype] name; even though they're just water molecules, genion must 
consider them differently.  So if you have some water molecules called "My_SOL" 
then copy spc.itp to my_spc.itp and rename the [moleculetype] as My_SOL.  Then 
in topol.top:

[ molecules ]
Protein  1
My_SOL   X
SOL      (Total water - X)



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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