nishap.patel at utoronto.ca
nishap.patel at utoronto.ca
Sun Jan 31 23:56:51 CET 2010
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
[ moleculetype ]
; Name nrexcl
[ 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
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
[ system ]
methane pair in water
[ molecules ]
; Compound #mols
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
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.
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.
>> 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
> 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
> 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
>>>> --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
>> Telephone: 416-978-1536
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Leslie Dan Faculty of Pharmacy
Department of Pharmaceutical Sciences
144 College Street
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