Dear Vishal,
Sorry - I mistyped. I meant 7 picoseconds (i have timestep of 0.002
picoseconds with SHAKE on).
Has this problem occurred before to anyone?
By the way, the .mdcrd file wrote was written out in the appropriate
format, with box size at the end, anyway..
On Fri, Jun 29, 2012 at 5:46 AM, Vishal Kumar Jaiswal
<vishal3990.gmail.com>wrote:
> 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 - 03:30:02 PDT
