make a figure of your rdf, post it online somewhere (I use
photobucket) and reply to the list with a link to your figure. Make
sure your figure is well labeled and give us a thorough description of
what you see that you don't like. Also tell us what your unit-cell box
vectors are. Also describe your system thoroughly, e.g. one methane in
a box of 100 water molecules...
I know that the meaning of "values fluctuate alot (i.e. decreasing)."
is immediately obvious to you, but for those of us who haven't seen
the graph it is pretty tough to figure out what is actually going on.
And off the bat, I'd say that the tail of your RDF is just poorly
defined (data coming from few waters in the figurative corners of the
unit cell for a central methane) and you are seeing the noise that
results from this -- Try regenerating your data by block averaging
into 0-33 ns, 33-66 ns, and 66-100 ns, then plot the average and
standard deviation of your results... I bet this will show you what's
going on.
Chris.
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.
I think this is a case where it is important to refer back to previous posts.
Is this related to your system that has one molecule of methane solvated in
water? If I recall, Chris already told you why the values you see
aren't smooth:
http://lists.gromacs.org/pipermail/gmx-users/2010-January/048297.html
Related to the volume issue, what type of pressure coupling are you applying?
Is your treatment of van der Waals appropriate (have you applied the switching
function properly)? Is switch appropriate for your chosen force
field? Are the
cutoff's you are using those prescribed by this force field? What is the
magnitude of the decrease in the volume? Is it systematic?
It is also important to be clear when posting - you are using "vdwtype
= switch"
and not "coulombtype = switch", hence the potential confusion when you say you
are just using switch. It makes a big difference. It is often most
convenient
to post your .mdp file instead of leaving it to guesswork.
-Justin
-Nisha
Quoting Will Glover <will_glover at yahoo.com>:
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, 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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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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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