[gmx-users] Density of the box

[Tsjerk Wassenaar]

Hi,

editconf needs to take the masses from a database file if not fed with
a run input file. It will probably miss out on some types of atoms or
get the masses wrong, especially with united atoms and/or dummies.
Probably the density would be correct giving a .tpr file for input.

Cheers,

Tsjerk

On Mon, Jan 10, 2011 at 4:06 PM,  <kavya at rishi.serc.iisc.ernet.in> wrote:
>
>
> Sir,
>
>   I am using Gromacs 4.0.7 version. Does this problem exits
> in other older or newer versions? what is the density of water
> that spc216 adds? If it is a fixed density, then i encountered
> a problem -
>
>
> I tried using 1 water molecule as a system (instead of protein), in a
> cubic box with 0.8nm distance (-d), and filled it with spc216 water,
> in this case the density it showed was 933.221g/l,
>
> --------------------------------------------------------------------
> Output configuration contains 513 atoms in 171 residues
> Volume                 :     5.48157 (nm^3)
> Density                :     933.221 (g/l)
> Number of SOL molecules:    171
> ---------------------------------------------------------------------
>
> but when I used the same system i.e water, with a cubic box of 1.0nm
> distact from water (-d) and filled with spc216 water it gave a density
> of 1001.85g/l,
>
> ----------------------------------------------------------------------
> Output configuration contains 1017 atoms in 339 residues
> Volume                 :     10.1226 (nm^3)
> Density                :     1001.85 (g/l)
> Number of SOL molecules:    339
> ----------------------------------------------------------------------
>
> So does this trend indicate that the density increases with increase in
> volume of the same system? and spc216 does not add water according to
> a specific density?
>
> With Regards
> MKS
>
>> Hmm, that's the second post in a week reporting editconf giving an
>> apparently spurious measurement of the mass. Sounds like it could be a
>> bug. Thoughts, anyone?
>>
>> Mark
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands