Think about a system of three molecules: A, B, and C. If A and B are the same,
they can share the same topology. If C is different, it needs a separate
topology. In the topol.top:
#include "A_B.itp"
#include "C.itp"
Otherwise, there is no special way to make and index group or anything else that
tells grompp/mdrun to only apply parameters to one group, but not another within
the same topology.
-Justin
Shaghayegh Vafaei wrote:
Hi all,
I am simulating 3 graphite slabs and I just want to charge one of them .
I edited the .itp file for the graphite slabs and I add some charges (negative
charges).
My problem is that I don't know how to specify that these charges just belong to
the first layer of three layers.
I was thinking may be I can categorized the slabs graphite molecules with
make_ndx in 3 different groups and I don't know what to do next.
So I appreciate if anybody can help me ,
Regards,
Shaqa
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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