Re: AMBER: Problem with Getting SHAKE to work

From: David A. Case <>
Date: Sat, 15 Sep 2007 22:05:55 -0700

On Sat, Sep 15, 2007, David Cerutti wrote:
> I was under the impression that all I had to do to turn on SHAKE in a
> pmemd dynamics run was set ntf = 2 and ntc = 2; however, when I do this I
> find that bonds containing hydrogen are still fluctuating. This creates
> problems, of course, when polar hydrogens come too near a negatively
> charged atom and cause the simulation to crash.
> Here is my input file. Can anyone suggest a remedy?
> ntc = 2, tol = 0.001, watnam = 'WAT ',

Where did the tol value come from? The default value is two orders of
magnitude smaller, and the recommeded value is three orders of magnitude

Tom C. and Tom D: can't we ever come to some decisions about default values
for this and for dsum_tol?


p.s. for purposes of SHAKE, hydrogens are defined as atoms whose name begins
with "H"...pretty lame, we should really look at the atomic mass.


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Received on Wed Sep 19 2007 - 06:07:02 PDT
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