I meant gradual heating not constant heating
On Fri, Jun 29, 2012 at 1:42 PM, Vishal Kumar Jaiswal
<vishal3990.gmail.com>wrote:
> Carlos,
> I think the options in Brandon's input file WILL perform a constant
> heating . I did a similar simulation ( heating from 0K to 300K with the
> same inputs and the temp reached to 300k in about 5.4 picoseconds )
>
> 0.000 0.00
> 0.200 62.83
> 0.400 105.09
> 0.600 137.55
> 0.800 164.46
> 1.000 182.86
> 1.200 205.31
> 1.400 224.02
> 1.600 228.46
> 1.800 241.73
> 2.000 253.39
> 2.200 262.48
> 2.400 260.94
> 2.600 269.21
> 2.800 266.20
> 3.000 276.66
> 3.200 284.18
> 3.400 283.72
> 3.600 283.19
> 3.800 292.74
> 4.000 287.69
> 4.200 291.04
> 4.400 290.79
> 4.600 291.18
> 4.800 289.07
> 5.000 299.28
> 5.200 296.97
> 5.400 301.01
>
>
> Vishal
>
>
>
> On Fri, Jun 29, 2012 at 12:42 PM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
>> 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 - 05:00:03 PDT
