Re: regarding ion concentration in implicit solvent

From: Nicholas M Glykos (
Date: Wed Feb 29 2012 - 08:29:40 CST

> So, is it necessary to neutralize the system even in implicit solvent
> and if so how?

System neutrality is necessary for the PME-PBC combination. Given that
(a) GBIS is incompatible with PME, and, (b) periodic boundary conditions
are not required with GBIS, it would appear that you do not have to
enforce neutrality.

> Also I need to know the implication of ion-concentration in an
> implicitly solvated system.

This appears to be in the 'Theoretical background' section of the NAMD
manual (look for 'Debye screening length').

            Nicholas M. Glykos, Department of Molecular Biology
     and Genetics, Democritus University of Thrace, University Campus,
  Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
    Ext.77620, Tel (lab) +302551030615,

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