On Fri, Jul 14, 2017, Li, Wen wrote:
>
> Thank you very much for your help! The prmtop file was generated, and
> minimization ncyc could run as long as it was set to run, such as 50000,
> but minimization with conjugate gradient failed after several thousands
> of steps. Is this an indication that the structure had problems if the
> first step of minimization with steepest descent results in VDWAALS =
> ************* even for a huge system?
What do mean by "failed"? Minimization in Amber (with default settings)
will very often fail after
several thousands of steps, giving a "LINMIN error" (Google on that, or
whatever error message you actually get. Such failures are generally of
little concern.
Look at the energies and structures you get from the minimization, to see if
there is evidence of any problems. Having bad energies at the first step is
quite common, and is (in fact) one reason for doing an initial minimization
in the first place.
....dac
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Received on Fri Jul 14 2017 - 18:00:03 PDT
