[gmx-users] changing charged groups in CHARMM RNA
mariagoranovic at gmail.com
Tue Mar 22 14:53:47 CET 2011
This must be specific to charmm's implementation in gromacs? Out of
curiosity, why can one not use charge groups ?
On Tue, Mar 22, 2011 at 2:45 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> 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 G.
>> Technical University of Denmark
> 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
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Technical University of Denmark
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