[gmx-users] Particle Insertion Method tpi - units and compensation of charged system

Kathleen Kirchner kirchner at mis.mpg.de
Thu Oct 13 12:53:42 CEST 2011

Dear all,

I'm using gromacs particle insertion method (integrater = tpi) to obtain
the excess chemical potential of single charged atoms.

On analyzing my results, two questions occurred to me:

1. The units for \mu_excess = -k_B T log <e^{-\beta U}>_N are given
according to tpi.xvg in kJ/mol*nm^3, which is kind of an energy density
and not an energy unit. So what does it mean? Is it normalized to any
volume? Maybe I'm missing some important point.

2. Is there a correction implemented for systems with a total net charge
not equal to zero? I'm trying to get the solubility of CO_2 in Ionic
Liquid, therefore I fear, the response of the system (which has zero net
charge) on inserting particles with 0.7 e and -0.35 e will be quite huge.

Best regards
Kathleen

--
Kathleen Kirchner
PhD student
Max Planck Institute for Mathematics in the Sciences
(MPI f. Mathematik in den Naturwissenschaften)
Inselstr. 22-26, D04103 Leipzig
e-mail: kirchner at mis.mpg.de
web: http://www.mis.mpg.de/scicomp/CompPhysChem/
Tel +49 341 9959 722
Fax +49 341 9959 999