On Tue, Dec 6, 2011 at 12:16 PM, Marc van der Kamp <marcvanderkamp.gmail.com
> wrote:
> Thanks Jason!
> I should have figured it wouldn't be all that easy to manually edit the
> prmtop.
> Yes, you did sent me parmed, thanks! I looked through the information of
> how to use it, and had a project student (for whose project this is) try it
> out. She used the following input (addexclusions.in):
>
> #Add exclusions to the exclusion list so that non-bonded interactions
> between mask1 and mask2 atoms are not computed.
>
> addExclusions :Na+ :Na+,Cl-
> addExclusions :Cl- :Na+,Cl-
>
You could combine these 2 into
addExclusions :Na+,Cl- :Na+,Cl-
It would be helpful to put the command "printDetails :Na+,Cl-" to see what
atoms are selected by the masks.
Also, can you send me the 2 topology files? (exclusions2.prmtop and the
original) so I can compare them? This was the same command I used
successfully in the email I sent above.
Thanks!
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Dec 06 2011 - 12:00:03 PST
