[gmx-users] Density of the box

[kavya at rishi.serc.iisc.ernet.in]

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
> --
> 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/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
>



-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.