I think the problem is from doing 0 steps of MD with Velocity Verlet versus
Leapfrog Verlet. The constraints might have been getting applied in a
different order and thus the input coordinates were probably different.
NAMD also does not separate forces and constraints the way amber does; it's
all or none.
Everything matches with no constraints, but I can't seem to match
everything when bonds with hydrogen are constrained. I am satisfied with
this nonetheless.
Brian
On Wed, Mar 18, 2015 at 11:50 AM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Wed, Mar 18, 2015 at 12:13 PM, Brian Radak <brian.radak.accts.gmail.com
> >
> wrote:
>
> > Ah yes, I forgot to turn on RATTLE in NAMD. I had already set ntf = 2 in
> > AMBER. Even so, the energies are a bit different:
> >
> > NAMD w/RATTLE "all": BOND = 277.4616
> > AMBER (ntf=2) : BOND = 272.9150
> >
> > By mdin is *very* minimal:
> >
> > &cntrl
> > nstlim=0, igb=6, ntf=2
> > /
> >
>
> You should set ntf=1 to make sure that all of the bond energies are
> computed.
>
> Note, ntf=2 does not turn on any constraints; ntc=2 does that. ntf=2 just
> saves time by not evaluating forces from the H-containing bonds.
>
> Then you need to make sure that NAMD does not "eliminate" any bonds
> similarly (as it seems you've already figured out).
>
> However, you can turn on constraints (ntc=2) *and* still have Amber compute
> the energies from the H-containing bonds (ntf=1); there's just not much
> point since those forces are effectively ignored, anyway.
>
> All the best,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Brian Radak
Postdoctoral Scholar
University of Chicago
Department of Biochemistry & Molecular Biology
Gordon Center for Integrative Science, W323A
929 E. 57th St.
Chicago, IL 60637-1454
Tel: 773/834-2812
e-mail: radak.uchicago.edu
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Received on Wed Mar 18 2015 - 10:30:02 PDT
