And get the use of radians right! Mark On Nov 15, 2012 4:01 PM, "Erik Marklund" <er...@xray.bmc.uu.se> wrote:
> Hi, > > 15 nov 2012 kl. 15.41 skrev Laura Leay: > > > Thanks Eric, > > > > Just to clarify (I hope this notation is in fact clear): > > > > E=0.5k [ 1 - cos( n*phi - n*phi_o +180 ) ] = 0.5k [ 1 + cos(n*phi - > n*phi_o)] > > ^ this whole equation is Dreiding ^this whole > equation is Dreiding converted to the form in Gromacs > > > > This would mean that: > > 0.5k in Dreiding = k in Gromacs > > n in Dreiding = n in Gromacs > > n*phi_o +180 in Dreiding (original form) is phi_s in the Gromacs > notation from the original post > > > > I think that's correct. > > > > > I hope this makes sense! > > > > Laura > > > > > > ________________________________________ > > From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on > behalf of Erik Marklund [er...@xray.bmc.uu.se] > > Sent: 15 November 2012 13:37 > > To: Discussion list for GROMACS users > > Subject: Re: [gmx-users] Dihedral form > > > > You could shift the reference angle by pi, which changes the sign of the > cosine. > > > > Best, > > > > Erik > > > > 15 nov 2012 kl. 14.25 skrev Laura Leay: > > > >> All, > >> > >> I would like to parameterise the Dreiding force field for use with > Gromacs. One thing I am not sure about is how to parameterise the dihedrals > >> > >> The Dreiding paper has the form; > >> > >> E= 0.5k { 1 - cos[ n( phi - phi_o)]} > >> > >> However I cannot find this form in the Gromacs manual. The closest I > can find in the Gromacs manual is: > >> > >> E = k [ 1 + cos(n*phi - phi_s) ] > >> > >> > >> Does anyone know of a way to use the Dreiding form in Gromacs, or to > convert to a form that is more suitable for use with Gromacs? > >> > >> Many thanks, > >> Laura > >> -- > >> 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 > > > > ----------------------------------------------- > > Erik Marklund, PhD > > Dept. of Cell and Molecular Biology, Uppsala University. > > Husargatan 3, Box 596, 75124 Uppsala, Sweden > > phone: +46 18 471 6688 fax: +46 18 511 755 > > er...@xray.bmc.uu.se > > http://www2.icm.uu.se/molbio/elflab/index.html > > > > -- > > 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 > > -- > > 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 > > ----------------------------------------------- > Erik Marklund, PhD > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: +46 18 471 6688 fax: +46 18 511 755 > er...@xray.bmc.uu.se > http://www2.icm.uu.se/molbio/elflab/index.html > > -- > 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 > -- 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