[gmx-users] dihedral potential structure

Филипп Орехов ofsmail at gmail.com
Sat Apr 4 17:51:07 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


A lot of thanks in advance.
With best regards/С наилучшими пожеланиями,
Orekhov Ph.S./Орехов Ф.С.
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