Thank you very much for your email, Justin. in case I want to use the reference parameters, which force-field and what should I do to get the .gro and .top files for this molecule?
Best regards, Cuong On 12 October 2012 21:14, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/12/12 8:04 AM, cuong nguyen wrote: > >> Dear Gromacs Users, >> >> I got the .gro and .top files of 1-octanol downloaded from PRODRG website. >> Please let me know if I can change charge, epsilon and sigma of the >> molecule as written in a paper? and How to do? >> >> > Atom types from PRODRG rarely, if ever, need changing. Charges can be > taken first by chemical homology (group-based approach that makes Gromos > force fields convenient) and then by calculating the charges yourself. For > 1-octanol, it should be very straightforward to obtain parameters, zero > charges on all the C atoms except for the one in the alocohol, then > standard alcohol charges for the C-O-H. Whether or not those parameters > are sufficiently accurate is up to you to decide, but that's the approach > one would take with this particular force field. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- 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
