seems ok- but be aware that this is NOT going to be gradual heating.
you've assigned a thermostate of 300K, which means the T will go to
300K very quickly. if you want to heat 0-300K, you need to slowly
change temp0. tempi just sets initial temperature and the thermostat
kicks in immediately.
can you paste the end of the sander mdout- from the last energy report
to the end?
On Fri, Jun 29, 2012 at 6:39 AM, Brandon Sim <simpavid.gmail.com> wrote:
> 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 - 04:00:04 PDT
