[gmx-users] RDF values lower than 1

[David van der Spoel]

Argyrios Karatrantos wrote:
> Hi, 
> i calculate the RDF from NVT simulation of a solution of polyelectrolyte chains and their counterions. The RDF calculated is between the monomers of the chains and the counterions.  I would expect that the equilibrated value of RDF would be 1. 
> However  it is always lower than 1,  at values of 0.9-0.95.   Whats the reason of that , is anything wrong with my simulation? 
> I do a long enough run to stabilize the total energy of the system and temperature
> Thanks in advance for your help

you may have vacuum in your system.

> 
> 
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se