Филипп Орехов wrote:
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)?
I'd guess they're just added. Set yourself up a simple example case to
test: only define the dihedrals, and evaluate energies (1-step EM) with
different dihedral constants.
Mark
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