[gmx-users] R-B dihedrals

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Apr 14 22:38:09 CEST 2015

Hi Alex,

Maybe writing out the preprocessed topology (grompp -pp) or checking the
.tpr with gmxdump can show whether the dihedral parameters are really what
you think they are.


On Apr 14, 2015 10:32 PM, "Alex" <nedomacho at gmail.com> wrote:

> I have a set of dihedrals described by the R-B potential, with a minimum at
> 90 degrees, and minimization indeed yielded angles very close to that.
> At some point, I decided to check if I can rotate the groups to another
> angle, say, 45 degrees. Simple enough, so I changed the expression. Energy
> minimization shows no difference -- still 90 deg. I turned off vdw for all
> atoms in the vicinity, set all charges to zero -- no difference. Hiked up
> the dihedral constant by three(!) orders of magnitude -- nothing.
> Commenting out these dihedrals immediately causes grompp errors, so they
> are definitely seen by the system (I tracked the errors to the atomtypes).
> The dihedral type (3) is listed correctly in the topology. A David Lynch
> mystery.
> Any ideas?
> Thanks,
> Alex
> --
> 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-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list