On Mon, Aug 01, 2016, Suguru ASAI wrote:
>
> Thanks for your suggestion and I'm sorry for late reply. It seems
> `ntc=2` fix the problem.
>
> But I'm wondering why only TIP4P-D requires this parameter while the
> Amber 14 manual said
>
> > Since SHAKE is an algorithm based on dynamics, the minimizer is
> > not aware of what SHAKE is doing; for this reason, minimizations
> > generally should be carried out without SHAKE. One exception is short
> > minimizations showse purpose is to remove bad contact before dynamics
> > can begin.
Your case falls under the "one exception" case: with a fairly good input
structure, it is generally possible to avoid SHAKE during minimization. But
this is not true if you have bad contacts or other problems with the initial
structure.
> So is my case an exception or `ntc=2` should be performed for the
> initial minimization step generally?
SHAKE should generally be used for an initial minimization (which, in fact, is
all that is required for most systems where MD is going to be performed
anyway. We should make the manual clearer about this.)
[Aside: someone could always fix the code to make minimization SHAKE-aware.
See the NAB code for how this can be done.]
....dac
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Received on Mon Aug 01 2016 - 08:30:03 PDT
