[gmx-users] Charging one layer of 3-layer slabs

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 10 21:08:15 CEST 2008

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.


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


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