Re: [AMBER] About NEB calculation form amber 11

From: Carlos Simmerling <>
Date: Mon, 8 Nov 2010 14:42:01 -0500

I'm having trouble understanding your question, so I apologize if this isn't
what you asked.
Force constants in calculations such as NEB, umbrella sampling and other
methods often need some trial and error to properly select. This is
especially true for large systems in explicit water, since they have not
been studied extensively with NEB. I suggest a test run with the values in
the tutorial. You want the force constant to be large enough to ensure that
you have even spacing of the replicas, but not so large as to cause the
simulation to be unstable.

On Mon, Nov 8, 2010 at 2:26 PM, Buddhadev Maiti <>wrote:

> Dear Sir / Madam,
> I am calculating NEB in explicit solvent for some large system. I am
> confused force constant about the atoms selected in NEB part. So my question
> is that NEB force constant is acting for different conformations or atoms of
> the different conformations in NEB selected. So what will be the suitable
> force constant as our system is large. Could you please reply me, it will be
> great help for me.
> Have a nice day,
> Thanks,
> Maiti
> _______________________________________________
> AMBER mailing list
AMBER mailing list
Received on Mon Nov 08 2010 - 12:00:03 PST
Custom Search