[gmx-users] Re: Density Deferences between spc216 and tip4p

[Tsjerk Wassenaar]

Chandu,

It's clear you didn't do the calculations. Please do them yourself and see
what answer you get for the density of 32885 water molecules in a box with
volume 10^3 nm^3. Note also that there may be implicit assumptions
underlying the value of the density provided by genbox, but it's the number
of molecules that counts.

Tsjerk

On Dec 13, 2007 11:04 AM, <csreddy at ncbs.res.in> wrote:

> Dear Jochen,
> Sorry to bother you. I did not calculate the densities it is the program
> output!. Is this a bug?.
>
> Regards
> Chandu
> > Message: 8
> > Date: Thu, 13 Dec 2007 10:28:02 +0100
> > From: Jochen Hub <jhub at gwdg.de>
> > Subject: Re: [gmx-users] Density Deferences between spc216 and tip4p
> >       water   models
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID: <4760FB22.3030101 at gwdg.de>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> > csreddy at ncbs.res.in wrote:
> >> Dear All,
> >> I was trying  create a  box (cubic 10 10 10) of water. I am a bit
> >> surprised by looking at the density deferences between spc216 and tip4p
> >> water models. I am giving the brief output below.
> >>
> >> genbox -cs tip4p.gro -box 10 10 10
> >>
> >> Output configuration contains 131540 atoms in 32885 residues
> >> Volume                 :        1000 (nm^3)
> >> Density                :     1639.65 (g/l)
> >> Number of SOL molecules:  32885
> >>
> > Theres is something wrong in your calculation of the density. From 32885
> > Molcules (18g/mol) in a volume (10nm)^3 I get a density of 982 g/l.
> >
> > Cheers, Jochen
> >>
> >> genbox -cs spc2i6.gro -box 10 10 10
> >>
> >> Output configuration contains 99678 atoms in 33226 residues
> >> Volume                 :        1000 (nm^3)
> >> Density                :     993.966 (g/l)
> >> Number of SOL molecules:  33226
> >>
> >> What would be the reason for this drastic differences in density? How
> >> can
> >> I make it into 1000 (g/l) by using above command.
> >>
> >> Thanks in advance.
> >> Regards
> >> Chandu
> >>
> >>
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> >> .
> >>
> >>
> >
> >
> > --
> > ************************************************
> > Jochen Hub
> > Max Planck Institute for Biophysical Chemistry
> > Computational biomolecular dynamics group
> > Am Fassberg 11
> > D-37077 Goettingen, Germany
> > Email: jhub[at]gwdg.de
> > ************************************************
> >
> >
> >
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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