Re: AMBER: Problem with Getting SHAKE to work

From: David Cerutti <>
Date: Sun, 16 Sep 2007 09:29:38 -0700 (PDT)

That was pointed out to me, and I have fixed it; don't know how it got so
small to begin with; I got the file from another run where it was set
correctly at 0.00001.

Fixing this, however, does not do much. Like I said earlier, however,
SHAKE does seem to work on the protein atoms (I tested this by removing
the bellymask I had on all protein atoms, to let them move a bit, and I
found that the hydrogen bonds lengths do indeed remain fixed); it's just
the solvent where I have a problem.

Nice to know about the hydrogen definitions.


On Sat, 15 Sep 2007, David A. Case wrote:

> 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
> smaller.
> Tom C. and Tom D: can't we ever come to some decisions about default values
> for this and for dsum_tol?
> ...dac
> 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.
> ...dac
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Received on Wed Sep 19 2007 - 06:07:08 PDT
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