ithu wrote:
I can't figure out how to put the coulombic potential only between
residues in chain A and residues in chain B, but not between residues
that are in the same chain.
You could look into energygrp_excl, but that will exclude *all* non-bonded
interactions, not just electrostatics. Otherwise, you may have to use tabulated
potentials or adjust the value of nrexcl in the topology (which will also affect
vdW, not just electrostatics).
-Justin
Thanks,
Esteban
2010/8/28 Justin A. Lemkul <[email protected] <mailto:[email protected]>>
ithu wrote:
Hi everybody,
I want to apply a coulombic potential between charged residues
in a coarse-grain model, but between residues that belong to
different chains of a protein complex. Both chains are name as
molecule A and molecule B in the topology file.
What specific problem are you having? In order to get useful
advice, you'll have to describe exactly what you're doing and why
it's not working when you think it should. A variety of models for
treating electrostatic interactions are available in Gromacs.
-Justin
Thank you very much,
Esteban
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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