Re: Err in equilibration run

From: Bill Ross <>
Date: Mon 22 Oct 2001 00:03:38 -0700 (PDT)

                  When i tried to minimize the system of DNA+water with
        constraints & then tried equilibration MD run, i am getting the
        following errs

        [shake failure]

        But on the otherhand if i do minimization for 2000 steps without any
        constraints & then do eqilibration MD run, i am not getting the
        above err. i don't understand why it is so.
Evidently the constraints used in minimization prevent a relaxation
that is critical to starting MD in the manner you have chosen. This
implies a problem with your starting coordinates, relatively minor
since minimization is capable of fixing it.

Bill Ross
Received on Mon Oct 22 2001 - 00:03:38 PDT
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