[gmx-users] How to examine our created topology

Justin Lemkul jalemkul at vt.edu
Sun Feb 15 14:04:58 CET 2015

On 2/14/15 5:21 AM, Faezeh Pousaneh wrote:
> Dear expert,
> I have created topology for an unstudied (simulation) molecule, and I can
> run it successfully.
> 1- How many or which quantities at least must be checked with experiment to
> become sure of the created topology? and if we find some difference with
> experiment, to what percent this differences can be acceptable? (for
> instance, if the experimental value of the density is 920 kg/m^3, is 1000
> kg/m^3 OK?).

That's a fairly large difference.  Typically agreement for bulk properties like 
these is 1-2% deviation for "good" force fields.

> 2- If we intend to improve the differences with the experimental values,
> what are the best ways? is changing slightly the charges on the atoms can
> be a good way (let us say we correctly have defined bonds, angels, ect
> according to the force filed)?

The real answer comes from what the force field parametrization protocol should 
be.  What force field are you using?  What did the developers do to parametrize 
the existing compounds in the force field?  For obtaining correct condensed 
phase properties, charges and LJ parameters are often tuned, but the relative 
contributions of these terms depend on the chemical nature of the molecule(s) 



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


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