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. Regards, Vijay.
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
