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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>>
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Received on Tue Aug 16 2016 - 13:30:02 PDT
