[gmx-users] PME, netcharge, implementation, counterions

David van der Spoel spoel at xray.bmc.uu.se
Fri May 14 13:13:04 CEST 2004

On Fri, 2004-05-14 at 12:02, Y U Sasidhar wrote:
> 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 ?
coulomb is negative, but van der waals is positive. you can not deduce
anything from that. but IIRC the implementation is directly from Darden
et al., including corrections.

> 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 ?
It is quite obvious because one usually only has a few ions. Then it
takes long before they sample the entire volume of the box. You could
say that the ions have reached equilbrium when the ion density in the
whole box is uniform when averaged over the simulation (or in fact the
density of all molecules in the box).

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone:  +46 18 471 4205  fax: +46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

More information about the gromacs.org_gmx-users mailing list