[gmx-users] surrounding a peptide by ions of magnesium
jalemkul at vt.edu
Thu May 2 13:35:40 CEST 2013
On 5/2/13 7:33 AM, Mohan maruthi sena wrote:
> Hi ,
> Thanks for a quick reply. Sorry for not being clear, I want to
> surround the peptide with just ions(sodium). How can I do this?
genbox -ci -nmol
You will need a coordinate file for a single Mg2+ ion to be inserted, which is
trivial to create by hand. I don't know how the ion force field parameters will
behave in the absence of explicit solvent. Are you planning to use implicit
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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