Dmitry,
My suspicion is that if you are setting ig=-1, you are happy with pure
randomness. The only reason I can see for reproducing these runs
'exactly' (modulo that parallel runs drift anyway due to varying order
of eveluation of expressions) is for debugging purposes.
Note that each successive run with -1 starts with no memory of where the
random generator left off. So why not continue from where you are,
unless you want all your file sizes to match or something?
The only important thing to preserve is your coords and velocities.
Not sure if that addresses your issues.
Bill
On 8/16/16 1:27 PM, Dmitry Suplatov wrote:
> Bill, thank you again for you time and help
>
> I want to clarify one last point.
>
> Setting ig of a restart run to a positive value used in the initial run is not incorrect, just not an entirely correct way to restart. Is it?
>
> I mean that since I use the rst file from the last step of the crashed run I will get a new trajectory (not a repetition of the first part of the run) even with the same sequence of "random" values. However, this new trajectory will be biased from a fundamental statistical point of view. Still, it most likely will be a fine MD trajectory. Would it?
>
> I simply wanna know if I should delete previous trajectories which were restarted by preserving ig from the previous run.
>
> Dmitry
>
>> On 16 Aug 2016, at 22:40, Bill Ross <ross.cgl.ucsf.edu> wrote:
>>
>> Putting it another way, I would likely start fresh from my last restrt with ig=-1, or rerun if I wanted tidyness.
>>
>> Bill
>>
>>> On 8/16/16 12:12 PM, Bill Ross wrote:
>>> The 'ig' value determines where the random number generator starts, so
>>> if the run restarts in the middle with ig from the beginning, the random
>>> numbers for the first part of the run will repeat.
>>>
>>> Is perfect reproducibility important?
>>>
>>> Bill
>>>
>>>
>>>> On 8/16/16 9:43 AM, DmitryASuplatov wrote:
>>>> Dear Amber users,
>>>>
>>>> I want to continue a crushed run. I use Langevin thermostat.
>>>> Do I understand correctly that in order to continue the trajectory
>>>> exactly as it would have ran if no crush occurred I need:
>>>>
>>>> - offset "nstlim" for the remaining number of steps
>>>> - set "ig" to the exact value used in the previous run (if I used -1 in
>>>> the previous run then I have to open the .out file and look for the
>>>> particular ig value there).
>>>>
>>>> Please comment.
>>>>
>>>> Thank you for your time.
>>>> Best,
>>>> Dmitry
>>>>
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Received on Tue Aug 16 2016 - 14:30:03 PDT
