[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 

#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)] + 
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.


More information about the gromacs.org_gmx-users mailing list