[gmx-users] extra non bonded interaction
koukoulas_th at yahoo.gr
Thu Jun 3 15:23:56 CEST 2010
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:
10 14 2 0 0 0 03.325789e-7
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.
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....
thanks in advance
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