[gmx-users] changing charged groups in CHARMM RNA

[Justin A. Lemkul]

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
> 

-- 
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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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