Initial MD equilibration: 20 ps, at constant volume, 0-300 K
&cntrl
imin=0,
irest=0,
ntx=1,
igb=0,
scee=1.2,
ntb=1,
cut=10,
nstlim=10000,
dt=0.002,
ntc=2,
ntf=2,
ntt=3,
gamma_ln=1.0,
tempi=0.0,
temp0=300.0
ntpr=100,
ntwx=100,
/
On Fri, Jun 29, 2012 at 6:24 AM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> can you reply with a copy/paste of your input file?
>
> On Fri, Jun 29, 2012 at 6:14 AM, Brandon Sim <simpavid.gmail.com> wrote:
> > 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 - 04:00:03 PDT
