[gmx-users] nonane solvent

[Justin A. Lemkul]

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

-- 
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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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