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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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