[gmx-users] PME-user for electrostatics

Berk Hess gmx3 at hotmail.com
Fri Nov 28 08:56:16 CET 2008


PME splits the calculation in a Mesh part and a direct space part,
which is normally 1/r minus the mesh part. Note that the mesh part
also contributes below the cut-off.
If you want something else than 1/r at short range
(you always have 1/r beyond the cut-off)
than you can just give the short-range potential you want,
mdrun takes care that it subtracts the short range
contribution of the mesh part.


> Date: Thu, 27 Nov 2008 13:37:36 -0800
> From: argyriosk at yahoo.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] PME-user for electrostatics
> hi, 
> i want to use a different function than the Coulomb to calculate the electrostatics 
> between charged ions. So i am thinking to user the PME-user option for the electrostatics.
> The manual says for the PME-user option"The PME mesh contribution is subtracted from the user table by mdrun".
> what that means?  should i have to add the short-range-potential (given by equation-4.33 in the manual)
> in the user table, because that will be subtracted with the mdrun? 
> please let me know,  and thanks a lot for your help
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