[gmx-users] Re: gmx-users Digest, Vol 114, Issue 15

[Mark Abraham]

On Mon, Oct 28, 2013 at 8:04 PM, Hari Pandey <harichem12 at yahoo.com> wrote:

> Dear Gromacs Users,
>
> First, I would like to thank Dr. Lemkul for reply.
>
> My problem description is as follows:
> I am using CHARMM36  forcefield to equilibrate of AOT. when I add the mass
> of all atoms from topology, it gives me 444.5 which is correct but when I
> run the script
>

Justin asked you about your atom names, but somehow you have forgotten to
answer him :-)


>
> editconf -c  -f A.gro -o A.gro   -density 1000  -bt cubic -box  5 -d 0.1 .
>
>
> It  display incorrect value for mass of input.  The mass of input should
> be 444.5 . The out come of above script is:
>
> Volume: 125 nm^3, corresponds to roughly 56200 electrons
> No velocities found
>     system size :  0.215  0.234  0.157 (nm)
>     diameter    :  0.287               (nm)
>     center      :  2.500  2.500  2.500 (nm)
>     box vectors :  5.000  5.000  5.000 (nm)
>     box angles  :  90.00  90.00  90.00 (degrees)
>     box volume  : 125.00               (nm^3)
>
> WARNING: masses and atomic (Van der Waals) radii will be determined
>          based on residue and atom names. These numbers can deviate
>          from the correct mass and radius of the atom type.
>

editconf only has a .gro file, so it does not know about any atom types, or
bonds, so it is not worth trying to write code to guess correctly whether
HG1 is the first hydrogen on the gamma carbon, or the first mercury, etc.
We do write a warning message, but sometimes people don't read them.

Mark


>
> Volume  of input 125 (nm^3)
> Mass    of input 967.25 (a.m.u.)
> Density of input 12.8493 (g/l)
> Scaling all box vectors by 0.234221
> new system size :  0.050  0.055  0.037
>     shift       :  1.914  1.914  1.914 (nm)
> new center      :  2.500  2.500  2.500 (nm)
> new box vectors :  5.000  5.000  5.000 (nm)
> new box angles  :  90.00  90.00  90.00 (degrees)
> new box volume  : 125.00(nm^3)
> Here we can see that mass of input is  967.25 which is far beyond the
> reality. this will cause error in density and all other mass dependent
> parameters.
>
> Please  help me how do I come over to this error
> Thank you so much for you kind help
>
> Hari
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