Hi justin, If you dont mind please give the link for gromacs 4 paper , it will surely help me to decide ff and parameter...
Thank you in advance, With best wishes and regards, Rama david On Sat, Nov 10, 2012 at 6:58 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/10/12 7:09 AM, Ali Alizadeh wrote: > >> Dear Rama >> >> Thank you for your reply dear Rama, >> >> I'm really sorry, >> >> My link was wrong, >> >> This link is correct: >> >> cinjweb.umdnj.edu/~kerrigje/**pdf_files/fwspidr_tutor.pdf<http://cinjweb.umdnj.edu/~kerrigje/pdf_files/fwspidr_tutor.pdf> >> >> Of course this tutorial do not use opls-aa but it says some of >> parameters about opls ff .(page-4) >> >> > I have no idea where these parameters come from (even the ones in Berk's > notes). I have never seen people use such settings with Gromos96, and > those listed in the table conflict with the protocols in the Gromos96 > literature. Settings for OPLS-AA are less clear. It is very common to use > 1.0-nm cutoffs (and in fact was the case in the Gromacs 4 paper), though > the original OPLS literature used different cutoffs depending upon what > types of molecules were present, which is not possible in Gromacs. You > should read lots of papers by people who use OPLS-AA for similar types of > systems and evaluate their success or inaccuracies. > > -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
