[gmx-users] An argument about long range electrostatics
hshallal at PACIFIC.EDU
Mon Feb 21 23:05:46 CET 2011
Dear Gromacs users,
While I was using Gromos force field in simulating a protein in explicit solvent, I used the following parameters:
rcoulomb = 1, rlist =1, rvdw = 1.4
Electrostatitcs : PME
VDW : Twin range cutoff
The above situation will not allow the calculation of any long-range electrostatics (LR-Coul) while calculating the energy of interaction among the specified energy groups of the the studied system.
I am facing the question of to what extent that could affect the accuracy of the calculation of the energy of interaction among the specified energy groups of the the studied system.
I argue that electrostatic interaction is mainly composed of H-bonds and salt-bridges, both with distance cutoffs of 0.35 nm and 0.4 nm respectively. So there should not be any need for calculating any electrostatic interaction beyond 1 nm (rcoulomb).
On the other hand, I came across another argument that calculating the long range electrostatics is "complicated by the practical limitations of dividing lattice sum energies into energy groups". I could not find any explanation of this point in the Gromacs manual! But I assume this kind of argument could be valid if ignoring the long range electrostatics would drastically affect the accuracy of interaction energy calculations mentioned above.
I would appreciate any feedback or comment concerning the above arguments.
Thanks a lot
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