[gmx-users] Potential energy

[Justin Lemkul]

On 3/20/18 2:40 PM, Alex wrote:
> Dear all,
>
> The potential energy of my system after two minimization steps (with and
> without constrained) is converging well, however, it is still positive
> around 1000 kj/mol !
> I think it is not a good sign for my system, but, what could be the reason
> and how I can overcome the issue? The system generated via "gmx
> insert-molecules" contains 1000 molecules of "C21H28O4".

Look at the individual values of internal (bonded) terms and nonbonded 
terms. Likely the intermolecular interactions are fairly weak, and the 
potential energy of the system is dominated by internal terms, which are 
by definition positive.

> Second question;
> To calculate the RDF between pair of atoms, let's say A and B, I was
> wondering if those two atoms should be differentiated in index.ndx file
> from beginning before invoking the gmx gromps?(similar to energygrps) or
> one can does the simulation without index.ndx and still possible to
> calculate the RDF between those two atoms?

There is no need for anything like energygrps. If you want to exclude 
the intramolecular contribution to the RDF (if relevant), you have to 
increase nrexcl in the topology and generate a new .tpr, otherwise 
everything is controlled by index groups.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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jalemkul at vt.edu | (540) 231-3129
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