Re: [AMBER] About NEB calculation from amber 11

From: Carlos Simmerling <>
Date: Mon, 8 Nov 2010 19:52:44 -0500

it's somewhat more complex than that, so I encourage you to look at the
code. The force constant is indeed used for all atoms in the mask, but it's
applied based on the projection of forces along the path tangent vector, so
not as simple as saying it is applied to all atoms. I encourage you to read
the Bergonzo et al IJQC paper on our implementation and the articles that we

On Mon, Nov 8, 2010 at 5:41 PM, Buddhadev Maiti <>wrote:

> Dear Amber users,
> Basically I would like to know whether in NEB calculations, as far as the
> force constant is concerned,
> the selected part of the different replicas can be regarded as a single
> effective "atom" or the force constant refers to
> individual atoms inside each selected region. Also, I would like to know
> what is the appropriate value of the force
> constant for a very large system such as mine (about 4000 atoms).
> Thanks,
> Maiti
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Received on Mon Nov 08 2010 - 17:00:03 PST
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