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
