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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Received on Wed Mar 18 2015 - 10:00:04 PDT
