[gmx-users] Turn off the electrastatic interaction between 2 energy groups
xhuang at chem.columbia.edu
Wed Feb 11 17:18:01 CET 2004
I already posted this question on the developer's list, but nobody answers it. So I posted it here again.
In Gromacs, "energygrp_excl" can exclude all non-bonded interactions between pairs of energy groups. But I only want to
turn off the electrastatic interaction between 2 energy groups.
The following is my idea. (I choose Cut-off for electrastatic calculation and use grid for the neighbour searching.)
There are 3 short range neighbour-lists generated in ns.c(vdw, coup, vdwc). It seems to me that "vdwc" will store the information of the
particls with both charges and the lj type. "vdw" will store the information of the particles whose charge is 0, and "coup" will store the information
of the particles whose lj is 0.(not sure?) What I have done is to loop over the charge groups and judge if the 2 groups are excluded, if they are,
I just add the particles in that group into "vdw" list instead of "vdwc" list. Then it seems to me that only vdw interaction is computed even if the
charge are not 0 for those particles.
But when I tested it, it did not work. Before I did the exclusion, the elecstatic intereaction of the system is 0.16 kj/mol, but after I chose the
exclusion, the elecstatic intereaction of the system is -201 kj/mol. It seems that the 1-2, 1-3 neigbours are even computed. (My system includes
1 spc water molecule and 1 pf6 molecule).
Do you know what is wrong with my idea, and is there a better way to do this?
Thank you very much!
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