Many thanks for your help. As for the 1-4 interactions, I am using the Gromos53a6 forcefield for everything apart from this particular dihedral.
I did not exclude 1-4 interactions previously with the multiple dihedral terms. Does this mean, if I use Ryckaert-Bellemans now (yielding the same potential function), I don't need to make any changes to 1-4 interactions ? Note that the previous method has been validated (with Gromacs 3.3), the problem is that it doesn't work with Gromacs 4 anymore. So I am trying to achieve the same result with Ryckaert-Bellemans instead of multiple periodic dihedrals. Many thanks Andreas ----------------------- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Berk Hess Sent: 28 May 2009 13:07 To: Discussion list for GROMACS users Subject: RE: [gmx-users] constant term in dihedral potential function > Date: Thu, 28 May 2009 21:49:45 +1000 > From: mark.abra...@anu.edu.au > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] constant term in dihedral potential function > > Kukol, Andreas wrote: > > Hi, > > > > I supply the multiple dihedral terms as a combination of single ones, such > > as: > > > > ;atom no. type phis k mult > > 22 23 24 25 1 180 7.470 1 > > 22 23 24 25 1 0 3.900 2 > > 22 23 24 25 1 180 1.100 3 > > 22 23 24 25 1 90 -5.685 0 > > I don't believe this works in the way you might expect. Page 109 of the > manual contradicts me, but (undocumented) dihedral type 9 was added > recently to allow multiple strictly-consecutive dihedrals of type "1" to > be accumulated on the same atoms. Anyway, this can readily be checked by > comparing 0-step EM runs, before and after commenting out the last of > the multiple dihedrals pre-grompp. Also, you can look at a gmxdump of > the .tpr. This works fine. > > > In case I supply the potential with a Ryckaert-Bellemans dihedral, do I > > need to exclude the 1-4 interactions between atoms 22 and 25 ? > > The form of the dihedral function doesn't matter. See section 5.4 of the > manual. If you set up the dihedral potential yourself, you choose if to use 1-4 or not. Your own force-field setup determines if to use 1-4's or not, not the technical way you supply the potentials in the topology. > > > Maybe one Ryckaert-Bellemans dihedral would be also computationally more > > efficient ? > > Maybe. Yes, RB will be computationally more efficient, but the time spent on it is probably negligible. Berk > > Mark > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ________________________________________ Express yourself instantly with MSN Messenger! MSN Messenger _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php