[gmx-users] rdf
Dallas B. Warren
Dallas.Warren at pharm.monash.edu.au
Mon Feb 1 01:17:41 CET 2010
A single methane molecule in water, it is not surprising at all that
there is some noise in the rdf produced. If you want it smoother than
that, you will simply having to run it for longer. The rdf is an
average, insufficient data points mean it will be noisy, you cannot get
around that fact.
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail.
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> bounces at gromacs.org] On Behalf Of nishap.patel at utoronto.ca
> Sent: Monday, 1 February 2010 9:57 AM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] rdf
>
> Hi,
>
> I saved my rdf plot as a pdf file and I have attached it to this
> email. Hopefully it will work. My system is one methane with 893
> molecules of tip3p water in a cubic box of size 3 3 3 (nm). My
> topology file is :
>
> ; Include forcefield parameters
> #include "ffoplsaa.itp"
>
> [ moleculetype ]
> ; Name nrexcl
> Methane 3
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass
> typeB chargeB massB
> 1 opls_138 1 METH C 1 -0.24 12.011
> ; qtot -0.24
> 2 opls_140 1 METH H1 1 0.06 1.008
> ; qtot -0.18
> 3 opls_140 1 METH H2 1 0.06 1.008
> ; qtot -0.12
> 4 opls_140 1 METH H3 1 0.06 1.008
> ; qtot -0.06
> 5 opls_140 1 METH H4 1 0.06 1.008
> ; qtot 0.54
>
> [ bonds ]
> ; ai aj funct c0 c1 c2
> c3
> 1 2 1
> 1 3 1
> 1 4 1
> 1 5 1
>
> [ angles ]
> ; ai aj ak funct c0 c1 c2
> c3
> 2 1 3 1
> 2 1 4 1
> 2 1 5 1
> 3 1 4 1
> 3 1 5 1
> 4 1 5 1
>
>
>
> ; Include water topology
> #include "tip3p.itp"
>
> [ system ]
> ; Name
> methane pair in water
>
> [ molecules ]
> ; Compound #mols
> Methane 1
> SOL 893
>
> and my grompp file at constant volume is:
>
> ; VARIOUS PREPROCESSING OPTIONS
> title = Methane in water
> cpp = /lib/cpp
>
> ; RUN CONTROL PARAMETERS
> integrator = md
> tinit = 0
> dt = 0.002
> nsteps = 50000000
> comm_mode = Linear
> nstcomm = 1
> nstxout = 10000
> nstvout = 10000
> nstfout = 0
> nstlog = 1000
> nstenergy = 1
> nstxtcout = 1000
> xtc_precision = 1000
> xtc-grps = System
> energygrps =
> nstlist = 5
> ns-type = Grid
> pbc = xyz
> rlist = 1.4
> coulombtype = pme
> rcoulomb = 1.4
> epsilon_rf = 1
> epsilon_r = 1
> vdw-type = cut-off
> rvdw = 1.4
> Tcoupl = V-rescale
> tc-grps = System
> tau_t = 1.0
> ref_t = 298
> Pcoupl = No
> Pcoupltype = Isotropic
> tau_p = 1.0
> compressibility = 4.5e-5
> ref_p = 1.0
> gen_vel = no
> gen_temp = 298
> gen_seed = 173529
> constraints = all-bonds
> constraint-algorithm = Lincs
> unconstrained-start = yes
> lincs-order = 4
> lincs-iter = 2
> lincs-warnangle = 30
>
> Does this makes sense? And Chris, I don't understand what you mean by
> defining tail of my rdf.
> -Nisha
>
>
>
>
>
> Quoting chris.neale at utoronto.ca:
>
> > 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
> >>>>
> >>>>
> >>>> --gmx-users mailing list gmx-users at gromacs.org
> >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >>>> Please search the archive at http://www.gromacs.org/search before
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> >>>>
> >>>
> >>>
> >>>
> >>> --
> >>> gmx-users mailing list gmx-users at gromacs.org
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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
> >
> >
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> posting!
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> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
>
>
>
> 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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