Hi Brandon
No this is not the expected behavior ,the simulation should complete the
number of steps ( nstlim)
By the way, with 3500 steps you are covering 7 nanoseconds which means a
step size of 2 picoseconds. i do not think it is acceptable.
you should have timestep of 0.002 picoseconds ( if you restrict hydrogen
movement by SHAKE , NTC = 2) or else use timestep of 0.001 picosecond.
Hope this helps
Vishal
On Fri, Jun 29, 2012 at 11:17 AM, Brandon Sim <simpavid.gmail.com> wrote:
> Dear Amber users,
>
> Does sander stop equilibration when temp0 is reached, even when the number
> of steps has not gotten to nstlim?
>
> I ran three simulations with nstlim=10000, but all three ended at step
> 3500, resulting in 7 nanoseconds of trajectory and 35 frames (I wrote a
> frame each 100 steps).
>
> The temperature had already gotten to ~300 K , which was my temp0. Is this
> expected behavior, is my script wrong somewhere?
>
> Thanks,
> Brandon
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Received on Fri Jun 29 2012 - 03:00:02 PDT
