[gmx-users] surrounding a peptide by ions of magnesium

Justin Lemkul 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.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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