[gmx-users] rdf

nishap.patel at utoronto.ca nishap.patel at utoronto.ca
Sun Jan 31 23:56:51 CET 2010


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 posting!
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>>>>
>>>
>>>
>>>
>>> --
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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
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> Please search the archive at http://www.gromacs.org/search before posting!
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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
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