nishap.pa...@utoronto.ca wrote:
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_glo...@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.pa...@utoronto.ca
<nishap.pa...@utoronto.ca> wrote:
From: nishap.pa...@utoronto.ca <nishap.pa...@utoronto.ca>
Subject: [gmx-users] rdf
To: "Discussion list for GROMACS users" <gmx-users@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
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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