AMBER Archive (2009)

Subject: [AMBER] Polarizable force field problem: non constant total Energy, EPOLZ is increasing

From: Tommaso Cupido (
Date: Mon Apr 27 2009 - 09:10:12 CDT

Hi there,
I'm trying to simulate a small peptide containing unusual residue in a water
I'd like to use the polarizable ff02.r1 or its EP version with a POL3 water
box, ca 3000 atoms

I generate the .crd and .top files in xleap
and did some simulation,

the problem is that when I try to run langevin, constant pressure, dynamics
with a 1 fs step,
despite an apparently normal 100 ps equilibration step
during the production dynamic
the total energy is increasing over and over
even after 5 ns simulation
this seems to be due to increasing EPOLZ energy from minus several thousands
to plus one thousand
temperature, pressure and volume as well as kinetic energy are constant,
but there are other weird values on other variable I wasn't able to
track down anything about

these are: dipole convergence, that is slightly increasing on the hundreds
ps scale ca 0.1E+00
 and the correlated temperature from 10 k to 200 K going up.

The same system works fine (mathematically) with the ff99SB forcefield

Has anybody run into a similar problem?
or has anybody a suggestion on what can it be the cause?

Thank you in advance


Tommaso Cupido
Institute for Research in Biomedicine
Chemistry and Molecular Pharmacology lab. (
Baldiri Reixac 10, 08028 Barcelona, SPAIN
phone: +34 934037127
fax: +34 934037126
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