[gmx-users] changing charged groups in CHARMM RNA

Justin A. Lemkul jalemkul at vt.edu
Tue Mar 22 14:45:21 CET 2011

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."


> Thanking you in advance
> Maria
> -- 
> Maria G.
> Technical University of Denmark
> Copenhagen


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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