[gmx-users] extra non bonded interaction

Mark Abraham mark.abraham at anu.edu.au
Fri Jun 4 01:37:52 CEST 2010

----- Original Message -----
From: Thanasis Koukoulas <koukoulas_th at yahoo.gr>
Date: Thursday, June 3, 2010 23:26
Subject: [gmx-users] extra non bonded interaction
To: gmx-users at gromacs.org

| > hello 
> I have a problem with C10O3H. The problem is that i use Trappe model and there you can add an extra repulsive interaction of molecule 10 (Oxygen) with molecule 14 (Hydrogen). The formula that TraPPE uses is 4E7/rij^12. with the transformation of 4E7in gromacs units (kJ*nm^12*mol-1) i take a numper 3.325789e-7 witch until now i put it in [pairs] with the sexond function like this:
> [Pairs]
> 10 14 2 0 0 0 03.325789e-7

This line doesn't seem to have enough fields (See table 5.4 of manual)

> the zeros i use is  for fudgeQQ because i dont want to have coulomb 14 in this pair and  charges of both of them for the same reason. it seem to work because at the end i have a coulombic energy 1-4 at a reasonable price but the total energy is not correct.

Construct a toy example (minimal single molecule in vacuo?) that will let you trouble-shoot what you are doing by computing by hand what the energy should be. Compare with GROMACS with and without this extra [pairs].

Be sure your combination rule paradigm is what you want it to be.


> please if someone can think smth answer me. The prices i get i can compare them with another researcher who did the same work with the use of monte  carlo. i am stucked for three months and i have read th manual over and and over again without result....

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