On Mon, Apr 27, 2009, Tommaso Cupido wrote:
> I'm trying to simulate a small peptide containing unusual residue in a
> water box I'd like to use the polarizable ff02.r1 or its EP version with
> a POL3 water box, ca 3000 atoms
>
> 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
This seems like a serious problem. It may be that the langevin
thermostat is increasing the kinetic energy of the dipoles. You don't
say much about what parameters were chosen, but you should try setting
indmeth=1, which does an scf calculation at each step, *or* set up your
system more like that in the $AMBERHOME/test/dna_pol, ubiquitin or
polarizable_water test cases, all of which have ntt=0 and indmeth=3.
Certainly try the non-EP version first -- it's never been clear to me
that the pol + EP force field was ever properly tested (others on the
list should chime in here with what they know about this.)
...good luck...dac
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Received on Wed May 20 2009 - 13:04:40 PDT
