[gmx-users] How to mention torsional parameter in toplogy

Tushar Ranjan Moharana tusharranjanmoharana at gmail.com
Thu Jul 2 23:44:41 CEST 2015

Hi everyone,

I want to simulate polyunsaturated fatty acid in GROMOS force field. I want
to consider certain torsional potential (as described by Michal Bachar et.
al. http://pubs.acs.org/doi/full/10.1021/jp036981u). In the paper they have
mentioned following potential functions which they got from quantum
mechanical calculations (in original paper there was some mistakes in the
equations which later got corrected, I am writing the revised equations)

V(φ1) = 3.350[1 + cos(φ1-180)] - 1.660 [1 + cos(2φ1-180)] + 7.333 [1 -
cos(3φ1-180)]

V(φ2) = -5.685 + 7.470 [1 + cos(φ2 - 180)] + 3.900 [1 + cos(2φ2)] + 1.100
[1 + cos(3φ2)]

V(φ3) = 0.034617 [φ3]^ 2

V(φ4) = -3.500 + 4.533 [1 + cos(φ4 - 180)] + 3.000 [1 + cos(2φ4)] + 1.550
[1 + cos(3φ4)] + 1.300 [1 + cos(Θ)]

Where φ1 to φ4 are shown in following figure and Θ is the torsion angle
between the vectors defined by the two double bonds.  Now my problem is How
I will use these potential function in my simulation. I guess I have to
define some [ dihedrals ] and [ exclusions ] but I am confused what exactly
the line will be in the [ dihedrals ] section of the topology.
Any suggestion will be most appreciable. Thanks for your valuable time.
[image: Inline image 1]

"A society with free knowledge is better than a society with free food"

Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB