[gmx-users] rdf

Will Glover will_glover at yahoo.com
Sun Jan 31 07:46:00 CET 2010

100 ns is overkill for those liquids.  It should be smooth enough at 1 ns, provided you average g(r) over every molecule.
What do you mean the volume decreases?  With time?

As for the cut-off, it's well known that switching Coulomb terms leads to artifacts, and increasing the cut-off distance doesn't necessarily make things converge.  See http://pubs.acs.org/doi/abs/10.1021/ct0502256 for example.

Use PME for electrostatics.


--- On Sat, 1/30/10, nishap.patel at utoronto.ca <nishap.patel at utoronto.ca> wrote:

> From: nishap.patel at utoronto.ca <nishap.patel at utoronto.ca>
> Subject: [gmx-users] rdf
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Date: Saturday, January 30, 2010, 9:45 PM
> Hi,
>   I am doing rdf's of simple molecules. I ran my
> simulation of water and methane for 100ns to get a smoother
> curve for the rdf. I am trying to determine the volume, and
> after a certain cut-off I would assume my values to be
> constant (i.e. volume), but the values fluctuate alot (i.e.
> decreasing). If I am using 'switch', from say 0.8-0.9,
> shouldn't the values smooth off after 0.9nm? and stay
> constant after that? Any insights would be helpful.
> Thanks.
> Nisha P
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