Re: [AMBER] CHAMBER and CMAP difficulty

From: Jason Swails <>
Date: Wed, 18 Mar 2015 12:50:17 -0400

On Wed, Mar 18, 2015 at 12:13 PM, Brian Radak <>

> 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

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 M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Mar 18 2015 - 10:00:04 PDT
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