Hi, I am not an expert, but I think there is no such tricky parameter for normal mode calculation though I don't know what your situation is.. You can find some tips at the below link.. http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis
If you set parameters extremely wrong the grompp program gives some notes and warnings that would help you a lot. An important thing is that you have to perform all the calculations with double precision. Yu 2014-07-29 15:37 GMT+02:00 xy21hb <xy2...@163.com>: > > > > > > > > > > > Dear all, > > > I wonder if there is anywhere I can know the details of mdp files used for > normal mode analysis. > I understand from the maunal that it needs steepest descent, conjugate > gradient, l-bfgs, nm in "md" options consecutively, > but I am not sure about other parameters set in these different stages. > > > Many thanks, > > > OAY > > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
