[gmx-users] Density of the box

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

Dear Gromacs users,

I was trying to run a simulation using a protein of 123  aa long
and wanted to adjust the density to 993.04g/l so with the following
command I ran the editconf:

editconf -f conf.pdb -o box.pdb -bt cubic -d 0.8 -density 997.0479

Its output was as follows:

--------------------------------------------------------------
.
.
Read 1842 atoms
Volume: 115.734 nm^3, corresponds to roughly 52000 electrons
No velocities found
    system size :  3.370  4.749  4.270 (nm)
    diameter    :  4.979               (nm)
    center      :  1.646  1.395  2.422 (nm)
    box vectors :  4.707  6.445  3.815 (nm)
    box angles  :  90.00  90.00  90.00 (degrees)
    box volume  : 115.73               (nm^3)
Volume  of input 115.734 (nm^3)
Mass    of input 42476.2 (a.m.u.)
Density of input 609.444 (g/l)
Scaling all box vectors by 0.848671
new system size :  2.860  4.030  3.624
    shift       :  1.893  2.106  1.234 (nm)
new center      :  3.289  3.289  3.289 (nm)
new box vectors :  6.579  6.579  6.579 (nm)
new box angles  :  90.00  90.00  90.00 (degrees)
new box volume  : 284.70               (nm^3)
....
---------------------------------------------------------------
My doubt here is it says that the Mass of input is 42476.2 (a.m.u.),
but the mass of protein is 13795.4 Da (according to the protparam with
sequence input). I am not sure whether protparam takes into account
hydrogens. Even with the inclusion of hydrogens (885), the molecular
weight will still be 14686.49Da. So how is 42476.2 a.m.u. comes?

Thank you all in advance
MKS


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