[gmx-users] Explicit Hydrogen LJ param

[Justin Lemkul]

On 6/15/15 11:57 AM, Marcelo Depólo wrote:
> Hi all!
>
> It might be a silly question, but I am wondering why explicit hydrogens do
> not have LJ parameters in Gromos forcefields (they are set 0), while HC
> hydrogens (aromatic) has some value:
>
> ;name at.num mass    charge ptype       c6           c12
>     HC    1      0.000      0.000     A   8.464e-05  1.5129e-08
>       H    1      0.000      0.000     A           0           0
>

In theory, the force field can be parametrized in any way that reproduces the 
target data.  It seems to be GROMOS convention to parametrize the heavy atom in 
the polar group to have LJ parameters that account for the attached H; the 
remainder of the interactions are electrostatic, which will dominate in such 
cases, anyway.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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