Re: AMBER: rms in nmode

From: David A. Case <>
Date: Fri, 1 Jun 2007 08:50:27 -0700

On Fri, Jun 01, 2007, Marie Brut wrote:

> After a minimization reached with a drms of 10-5 with sander, I try to make a
> normal mode analysis with Nmode. But I get the message :
> Root-mean-square gradient of input coords is 3.7924497503677114
> This is greater than the requested maximum: 1.0E-5
> Can you tell me what is exactly the "Root-mean-square gradient of input coords"

The "gradient" is a vector containing the derivative of the potential energy
with respect to atomic coordinates. The RMS gradient is the root-mean-square
of the elements of this vector.

> Does it mean my calculation is wrong ?

Yes. Check the energy in nmode vs. that is sander...they are probably very
different. My guess is that you are being bitten by the fact that the default
value for scee is 2.0 in nmode, whereas the default is 1.2 in sander. If so,
the energy differences will show up in the 1-4 eel component.

The "drms" variable in nmode is what determines that maximum allowable
gradient. This is not well documented in the manual. But you need first to
get the energies in nmode and sander in sync with each other.

...good luck...dac

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Received on Sun Jun 03 2007 - 06:07:38 PDT
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