[gmx-users] How to mention torsional parameter in toplogy
mark.j.abraham at gmail.com
Fri Jul 3 00:28:25 CEST 2015
The functional forms available are in chapter 4 of the reference manual,
and the way to specify the parameters is in chapter 5. So perhaps after
some trig, you should be good to work that out (if not, then tabulated
bonded interactions are also possible). Make a trivial test case whose
energy will tell you that things are working like you expect.
On Thu, Jul 2, 2015 at 11:45 PM Tushar Ranjan Moharana <
tusharranjanmoharana at gmail.com> wrote:
> 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
> 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 -
> 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
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