[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 
electrostatic effects"
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 ?

2. Counterions:

"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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