[gmx-users] Fwd: A doubt from topology creation in Gromacs

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Apr 1 07:04:28 CEST 2015

---------- Forwarded message ----------
From: "Rakesh Pant" <rakeshkmc at live.com>
Date: Apr 1, 2015 1:13 AM
Subject: A doubt from topology creation in Gromacs
To: "tsjerkw at gmail.com" <tsjerkw at gmail.com>

 Dear Tsjerk,

I got your email id from gromacs user list. I have a doubt from gromacs
topology creation, on dihedral coefficients.

Suppose we have, and angle A-B-C-D, and we have parameters for this one
dihedral angle:

n       Vn             f1
1      -2.64           0.0
2     -0.811          0.0
3      0.949          0.0

(Vn=Vn/2*(1+cos(n*chi + f1)), ; Vn kcal/mole ; fn: degrees.

How can we use these parameter to get dihedral coefficients to use in
gromacs with fucntion 3. Or else if we use it with fucntion 1 can we take
any one of the three values given.


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