[gmx-users] gromos forcefield
rob yang
nextgame at hotmail.com
Tue Jan 10 15:52:31 CET 2006
hi list,
for the torsional dihedral parameter section in the gromos force field, i
noticed that all the defined torsions have only 1 term describing it.
According to the paper, the sugar rings should have multiple terms
describing it. Using the paper as reference, I found 4 dihedral angles
describing the sugar in the gromos parameter files, 53a6, supported by
gromacs:
#define gd_3 1 180.000 4.970 1
#define gd_5 1 180.000 9.350 1
#define gd_35 1 0.000 7.690 3
#define gd_37 1 0.000 9.500 3
my questions are:
1) Am I correct in interpretating that all 4 terms together describe *ONE*
OA-CHn-CHn-OA torsion?
ie, E= 4.97*[1+cos(1*T-180)] + 9.35*[1+cos(1*T-180)] + 7.69*[1+cos(3*T-0)] +
9.5*[1+cos(3*T-0)]
where T is the torsion angle in my structure.
2) Or, is it really there are 4 possibilities, pick only 1 of them to define
your given OA-CHn-CHn-OA torsion?
3) if 1) is correct, how should I use all 4 torsion parameters to define 1
torsion angles in my .top file? The conventional way is:
i j k l gd_3
Now how can I incorporate all of my torsion parameters to i j k l?
Thank you very much in advance.
rob
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