[gmx-users] energy terms during minimization

Ester Chiessi ester.chiessi at uniroma2.it
Wed Nov 20 16:55:01 CET 2002

Hi all,

During the energy minimization of my system ( an oligomer of poly(vinyl
alcohol)) in a water box, I noted some anomalies:

with sd and emtol 1000, the energy contributions 'bond', 'angle', 'dihe',
'LJ(1-4)', 'Coulomb(1-4)' increase while LJ(SR) and Coulomb(SR) decrease
and govern the trend of the potential energy
('bond' increases from the step 0 of about 5000 kJ/mol, 'angle' of about
3000, LJ(SR) decreases of about 10000 and Coulomb(SR) decreases of about

If I reduce the box size, the energy increases are smaller and seem
proportional with the box size.

If I perform the minimization in vacuo ( with no pbc) energy trends are
more 'regular' (with a small increase of dihe and Coulomb(1-4)).
When, in vacuo, I stress the convergence criterium to 100, the energy
contributions show maxima and minima.

Perhaps it's important to note that the oligomer starting structure is
already very near to a 'minimum' structure.

My question is:

Should I have to consider these results a 'warning' for the correct
simulation of the system?
Or, if the final geometry is correct, can I go on with the dynamics?

P.S. I tryed, as control, the minimization of the pure water box. I was
surprised the LJ and Coulomb were always 0. Why?

Thanks for any help


Ester Chiessi
Dipartimento di Scienze e Tecnologie Chimiche
Universita' di Roma "Tor Vergata"
Via della Ricerca Scientifica
00133 Roma (Italy)
e-mail: ester.chiessi at uniroma2.it
Phone: 39*6*72594462

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