Hello people,My professor and I tried to use the FENE potentials to relax a
protein from a unstable configuration for publishing paper. However, these
potentials didn't seem to work. Checking both the manual and the code of the
GROMACS software package for moleculair dynamics we found some things we do not
understand both me as even my professor.First one thing: In file bondfree.c in
gmxlib the force constant kb (parameter: real kb) for the FENE potential is
not included anywhere in the force neither potential calculation . bm =
forceparams[type].fene.bm; kb = forceparams[type].fene.kb; bm2 =
bm*bm; omdr2obm2 = one - dr2/bm2; vbond = -half*bm2*log(omdr2obm2);
fbond = -bm/omdr2obm2;Second one next thing:In the following lines:The
scalar force is composed over its dimension by dx[m]:fij=bond*dx[m]However in
stead of taking a unit normalized vector the original connecting vector is
taken. The manual isn't clear about this either, but looking at the equations
it doens't make a lot of sense to me and my professor to use the original
connecting vector.Greetings from China,Jiang
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