[gmx-users] PME, netcharge, implementation, counterions
Y U Sasidhar
sasidhar at chem.iitb.ac.in
Fri May 14 12:02:11 CEST 2004
1. PME and net charge
"Molecular dynamics simulations of biomolecules: Long-Range
Sagui C, Darden TA
Annu. Rev. Biophys. Biomol. Struct. 1999,28:155-79
Based upon the articles like the above ones, I understand
that to solve poisson equation for a periodic potential the
unit cell ( which is repeated ) must be neutral. Therefore
if any net charge is present a neutralising uniform charge
density is to be added to avoid infinite electrostatic
potential. This is supposed to fix "zeroth order" term
without disturbing higher order terms.
In a simulation of our peptide with **net charge** in spc
water using gromos96 ff and PME, I find that the TOTAL
coulomb energy ( of peptide + water full system )is always
**negative**, though coul14 energy is positive. Coul14
contribution is small ( .1 % ). This kind of result is
obtained on other systems with net charge also. So I take it
that Gromacs PME implementation takes care of "net charge".
Is this correct ? What reference can I cite to this effect ?
"If neutralsing cunter ions are added the equilibration
times tend to be longer."
I have come across this kind of observation in a couple of
papers but the statement was not referenced. Can you pl
point me to a reference ?
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