maria goranovic wrote:
Dear List
I was looking at the charged groups in a charmm nucleotide, and could
see several groups containing 4 to 14 atoms with integer charges.
However, the default topology does not have these charged groups. each
atom is given a charged group in the default topology. Can we foresee
any problems in replacing the default charged groups generated by
pdb2gmx by custom-made charged groups of integer values ? Along the same
lines, will this lead to a significant increase in performance, besides
the advantage of transferability ?
With the CHARMM force field, you should not use charge groups. Each atom should
be its own "group."
-Justin
Thanking you in advance
Maria
--
Maria G.
Technical University of Denmark
Copenhagen
--
========================================
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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