And if you turn off your restraints?
On Wed, Mar 29, 2017 at 1:26 PM, Sadegh Faramarzi Ganjabad <
safaramarziganjabad.mix.wvu.edu> wrote:
> David,
>
> > You had said in an earlier email that the second simulation "had no water
> box". I was asking for the evidence that led you to that conclusion.
>
> Well I don't see any water box when I load the output on VMD. It is only an
> abnormal structure with a bunch of carbon-like atoms.
>
> > Run a short "second" simulation with ntpr=1. Then you can try to find
> out whether the problems arise at the first step or later.
>
> I tried that; it gives the same output. It seems the problem starts from
> the beginning.
>
> Thanks,
> Sadegh
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 29 2017 - 13:00:02 PDT
