[gmx-users] nonane solvent

Vijayaraj vijayaraj81 at gmail.com
Tue Oct 25 18:43:34 CEST 2011


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.

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