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 torsional 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, Utot=0.25*(U1+U2+U3+U4)?
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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