[gmx-users] Re:density vs time
Vitaly V. Chaban
vvchaban at gmail.com
Wed Mar 17 16:03:56 CET 2010
I mean the volume of the MD cell for NVT ensemble. How did you obtain
it? Just replaced one water with one methane molecule?
Anyway, I think your RDF is correct.
> What do you mean the value for methane? As in the charges? This is my
> topology file and I am using OPLS-AA for methane.
> 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
> 2 1 3 1
> 2 1 4 1
> 2 1 5 1
> 3 1 4 1
> 3 1 5 1
> 4 1 5 1
> My RDF does look reasonable and the peaks are okay with the values
> published earlier, but because of what I am calculating (i.e. volume),
> it seems to be very sensitive and even 0.01 makes a difference.
> Thanks for suggestions.
> -Nisha P
> Quoting "Vitaly V. Chaban" <vvchaban at gmail.com>:
>>> I am trying to get an rdf graph actually, and my values are very close
>>> to one, but not exactly one, and I was wondering if there is some
>>> normalization issue with g_rdf? These are my values for rdf:
>>> Near the end, the values are fluctuating around one. The reason I was
>>> trying to get density values was may be to try an understand if the
>>> density computed by gromacs is different for just water system and
>>> water+one methane system (i.e. gromacs calculates the density using
>>> the box and total number of molecules in the box, which would be fine
>>> for water system but for methane+water it would slightly be a little
>>> different, no?) and may be normalize my rdf using the difference in
>>> the density factor. Does that make sense?
>> If you don't use barostat, the density of the system is fixed by
>> yourself. g_rdf uses it to calculate the average particle density in
>> the box. Your rdf seems very reasonable as for me.
>> This is another question how you selected the concrete value for
>> methane in water system...
>> Dr. Vitaly Chaban
More information about the gromacs.org_gmx-users