I think the most extensive calculations using various amber-pol FF have
been done for DNA, DNA-complexes:
Baucom et al. JCP, 121,6998 (2004)
Babin et al. JPCB, 110, 11571 (2006)
Vladimirov et al. JPCB,113,4425 (2009)
They discuss how they setup calculations and what troubles did they
encountered.
In general - ff02 was slightly better than nonpolarizable amber-ff
and ff03EP was worst, and least stable.
Other tests for proteins - were usually quite short, thus not much
conclusive yet, but EP's could not inferfere that much with the structure
as in the case of DNA/RNAs.
Piotr
On Mon, 27 Apr 2009, David A. Case wrote:
> From: David A. Case <case.biomaps.rutgers.edu>
> Sender: amber-bounces.ambermd.org
> To: AMBER Mailing List <amber.ambermd.org>
> Date: Mon, 27 Apr 2009 13:30:55 -0400
> Subject: Re: [AMBER] Polarizable force field problem: non constant total
> Energy, EPOLZ is increasing
> Reply-To: AMBER Mailing List <amber.ambermd.org>
>
> 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 - 13:05:39 PDT
