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 [email protected]:
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 switchingfunction 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 youare 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 posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php-- 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! 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.phpNisha 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 [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users 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 [email protected]. 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
meth.jpg.pdf
Description: Adobe PDF document
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