[gmx-users] dihedral potential structure

Филипп Орехов ofsmail at gmail.com
Mon Apr 6 09:46:36 CEST 2009

Hello gromacs users,

I want to ask a simple thing, which nevertheless is not really clear to me,
but it's sometimes too important. For instance, I have in my molecule
angle around a double bond: -C-C(H)=C(H)-C-. The dihedral potential contains
following four parts:
-C-C=C-C-, a U1 from topology
-H-C=C-C-, a U2=U3 from topology
-C-C=C-H-, a U3=U2 from topology
-H-C=C-H-, a U4 from topology
Attention please, here the question is:  how  does the final potential look
like?  Is it just only a sum
Utot=(U1+U2+U3+U4) or gromacs divides it on the number of elements of the
dihedral, I mean, in this case,

A lot of thanks in advance.

With best regards/С наилучшими пожеланиями,
Orekhov Ph.S./Орехов Ф.С.
Department of biology, Moscow University
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