[gmx-users] how to remove an energy contribution in gromacs?
Jones de Andrade
johannesrs at gmail.com
Mon Aug 6 14:49:26 CEST 2007
Well, I'm trying to calculate an <E> energy from my simulations, where <E>
here stands only for the sum of *intermolecular* vdw and coulombic terms,
and LJ(1-4) and coul(1-4). This means that I should find a way to exclude
any "1-5", "1-6", "1-7" and so on contributions for coulombic and vdw
energies, which I guess are included in the SR terms if the rcut is long
I though on doing it by use of a modified topology (with an arbitrary
increased "nexcl" term) after the simulation is completed just for a
"-rerun" job, and then use the g_energy program to calculate these
Unfortunatelly, for some reason I'm not getting the correct values by large
differences. Properly saying, only doing the above described procedure is
yelding me even modifications in the bond, angle and dihedral terms of my
simulations, which should not vary in a rerun with new nexcl values.
Moreover, all energy terms with no exception seem to be only divided by a
factor around 10., in comparison with the simulations with the original
I'm pretty sure I'm missing something here, but I have no idea of what could
it be. Could someone please help me with this matter somehow?
Thanks a lot in advance.
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