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From: Irene Newhouse (einew_at_hotmail.com)
Date: Tue Mar 31 2009 - 16:48:34 CDT

I have this sinking feeling that I'm going to be embarrassing myself publically & archivally,

but I'm stuck, so here goes....

 

The gromacs manual page, page 50, gives the L-J potential as c12/r**12 - c6/r**6

which corresponds to the 'alternate' formula given on the L-J potential wikipedia page, which

also states that this is the formulation usually used in simulation programs: A/r**12 - B/r**6.

I deduce, perhaps incorrectly, that LJ-a in the dowser remarks below refers to A above, which is

therefore equivalent to c12 given use of the same system of units, and that c6 & B are equivalent.

The potential has to have units of energy, so A & B must have units such that A/r**12, etc.,

has units of energy. The gromacs manual page 64 indicates gromacs uses kJ. I infer that dowser

uses kcal because the 1996 Proteins paper reports values in kcal/mol. Gromacs, as you so helpfully

noted, uses nm, which need to be multiplied by 10 to get to Angstroms, which again appears

to be used in dowser, as that is the unit in the Proteins paper. However, these

two factors do not convert the gromacs values for N into the dowser values, so I'm still missing

something.

 

Can anyone help me out, please?

 

Thanks!

Irene Newhouse

 

> > This is in dowser:
> >
> > REMARK atomtype LJ-a LJ-b MS-radius
> > TYPE N 49.36 1300.0 2.40 # any Nitorgen
> >
> > While the closest thing I can seem to find is in ffmgxnb.rtp, where
> > the apparently relevant
> > comment line reads:
> >
> > ;name at.num mass charge ptype c6 c12
> > & N reads:
> > N 7 14.00670 0.000 A 0.24362E-02 0.16924E-05
> >

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