[gmx-users] File editing - only one layer of water around a molecule

Justin A. Lemkul jalemkul at vt.edu
Tue May 1 22:26:36 CEST 2012

On 5/1/12 4:12 PM, Lara Bunte wrote:
> Hi Justin
> Thanks, that makes sense. I have the group "Close to ISO" that contains the water molecules in my specified region and I have the group ISO and therefore the next step is to unite this two groups.
> If I typed
> make_ndx -f molecule.pdb -n index.ndx -o index_new.ndx
> the make_ndx program shows only one group, the "Close to ISO" with number 0 and no other groups, so how to merge them?
> I typed l for "list residues" and than there was ISO and SOL.
> Now if I am at this place, how to tell GROMACS, that ISO is a group also, that I can merge it with "Close to ISO"?

My recollection of this feature was wrong; sorry.  I assumed the default groups 
would be appended to your custom index group, which is not the case.

Create a new index group with:

make_ndx -f molecule.pdb -o index2.ndx

This will contain groups like ISO and SOL.  Then just concatenate the existing 
index groups:

cat index2.ndx index.ndx > index3.ndx

Then attempt to do what I said before, operating with index3.ndx, i.e.:

make_ndx -f molecule.pdb -n index3.ndx -o index_final.ndx

where index_final.ndx will have the merged groups.



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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