[gmx-users] Re:density vs time

[Vitaly V. Chaban]

Hi Nisha,

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.

Vitaly


>
> 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
>       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
>
> 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?
>>>
>>> -Nisha
>>
>> 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
>>