Justin A. Lemkul
jalemkul at vt.edu
Sun Jan 31 21:47:43 CET 2010
nishap.patel at 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:
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.
> Quoting Will Glover <will_glover at yahoo.com>:
>> 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
>>> 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.
>>> 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
> Telephone: 416-978-1536
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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