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 - 03:30:03 PDT
