[gmx-users] Dihedral angle restraints in NMR refinement...

Volker Knecht vknecht at gwdg.de
Wed Sep 25 15:23:47 CEST 2002

    Hello Chris,

> I have been playing a little bit with the NMR derived dihedral angle
> restraints as defined as impropers. I ran into the following problem:
> Dihedral angle restraints close to 180 degrees give rise to local
> heating and a lot of LINCS warnings (and exploding system).
> On page 59 of the gromacs manual it is stated that impropers should be
> defined as far away from 180 degrees as possible. The reason (dank je
> Bert!) is that the periodicity is absent and small changes in the
> dihedral angle leading to flips from ~-180 to ~+180 lead to huge
> differences in improper dihedral energy.

> So I was hoping someone of the developers-team could help us (the NMR
> users) with this.

Without extending the gromacs code, you could use periodic dihedral
restraints by defining extra proper, cosine-based dihedrals

    V(phi) = k [1+cos(n phi - phi0)]

with a multiplicity

    n = 1


    phi0 = alpha+180

Best regards,
Volker Knecht

-------------- next part --------------
A non-text attachment was scrubbed...
Name: vknecht.vcf
Type: text/x-vcard
Size: 438 bytes
Desc: Card for Volker Knecht
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20020925/9f95693d/attachment.vcf>

More information about the gromacs.org_gmx-users mailing list