[gmx-users] Manual Counterion Placement

Justin A. Lemkul jalemkul at vt.edu
Mon Sep 19 01:54:20 CEST 2011

Marc Charendoff wrote:
> Hello,
>         I  would like to manually place a counterion into my system with 
> the genion command for which I am pretty sure I will need an index file. 
> My question is how to properly select the specific water atoms / or SOL 
> residue(?)  number  (that I get from my pdb or gro file)  so that it 
> comes up as an option when I run genion. I looked at the make_ndx 
> options, but they weren't too clear to me. Guidance appreciated.

The only way to do this is to replace one molecule at a time; genion isn't 
designed for such replacements.  Probably the easier method is to use a text 
editor to replace the OW atom with the desired atom and delete the extraneous HW 
atoms.  Otherwise, you have to make an index group for each water to be 
replaced, run grompp and run genion.  The latter is far more work than the former.



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


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