[gmx-users] nonane solvent

Justin A. Lemkul jalemkul at vt.edu
Tue Oct 25 20:06:06 CEST 2011

Vijayaraj wrote:
> Hello,
> I need to simulate a peptide in nonane solvent environment using ff99SB 
> force field. As there are different procedures used to create a solvent 
> box, different from water, specific to several force fields, I would 
> like to make sure the method which I am going to use will be appropriate 
> for my simulation. here is the procedure,
> 1. Nonane parameters using GAFF with python interface to antechamber 
> (acpype), this program generates gromacs compatible amber ff.
> 2. solvent box with nonane using gromacs with appropriate box dimension 
> and NPT equilibration.
> 3. Insertion of the peptide to the equilibrated nonane solvent box.

This seems reasonable to me.



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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