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 - 06:07:02 PDT
