Hi Will,
I have been using pme from the very start and it didn't help with
the volume. Could you please elaborate on what you mean by average
g(r) over every molecule?
And because my rdf-s are not smooth enough even with 100ns, I get
fluctuating data using rdf-s.
-Nisha
Quoting Will Glover <[email protected]>:
Hi,
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.
Regards,
--
Will
--- On Sat, 1/30/10, [email protected]
<[email protected]> wrote:
From: [email protected] <[email protected]>
Subject: [gmx-users] rdf
To: "Discussion list for GROMACS users" <[email protected]>
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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Nisha Patel
MSc Candidate
Leslie Dan Faculty of Pharmacy
Department of Pharmaceutical Sciences
144 College Street
Room 1172
Toronto, ON
M5S 3M2
Canada
Telephone: 416-978-1536
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