[gmx-users] Potential energy
jalemkul at vt.edu
Tue Mar 20 20:02:25 CET 2018
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 A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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