Dear Adrian,
thanks for the response.
So, the random number generator is not used for the assignment of
*initial* velocities?
Since I specified TEMPi=50.0, all atoms receive a certain initial
velocity value, and there, I thought up to now, the random number seed
ig would be in effect, too.
(In this case, I used an explicit ig value /=0 to maybe have a
'reproducible' random number, but this does not matter here...)
Best regards,
Anselm
Am 04.02.2022 um 18:10 schrieb Adrian Roitberg:
> Hi Anselm
>
> ntt=1 just check the temperature at the last step, and rescales EVERY
> velocity in the system by a factor, to get T to what you want it.
>
> There is no random number being used at all when you do ntt=1, so the
> runs will be identical in your case.
>
> ntt=2 (andersen) and ntt=3 (Langevin) use random numbers so you should
> see a difference.
>
> BTW: you can change the random numbers by hand, like you did, or you can
> choose ig=-1 and let Amber choose one for you.
>
> The second way is preferred, so you are sure you will get a different
> number every time you run.
>
> Adrian
>
>
> On 2/4/22 12:01 PM, Dr. Anselm Horn wrote:
>> [External Email]
>>
>> Dear Carlos,
>>
>> I did not read in any velocities, since I used a structure from a
>> minimization. The thermostat was NTT=1.
>>
>> Do I miss something?
>>
>> Best regards,
>>
>> Anselm
>>
>>
>> Am 04.02.2022 um 16:00 schrieb Carlos Simmerling:
>>> which thermostat did you use? also, did you read velocities from the
>>> input
>>> coordinates? these are two places that can be affected by the seed.
>>>
>>> On Fri, Feb 4, 2022 at 9:09 AM Dr. Anselm Horn <anselm.horn.fau.de>
>>> wrote:
>>>
>>>> Dear Amber experts,
>>>>
>>>> I have a short question regarding the random number generator for
>>>> initial velocities (TEMPi) on GPUs:
>>>>
>>>> I ran two MD simulations in a periodic solvent box starting from a
>>>> minimized structure, with weak-temperature coupling (NTT=1) and an
>>>> initial temperature of 50 K (TEMPi=50.0); for each simulation, I used
>>>> an explicit, but different random number seed (ig=NNN). I used the
>>>> executable pmemd.cuda_DPFP (Amber20, patch12) on a A40-GPU, since my
>>>> original intention was to test whether system relaxation might be save
>>>> on GPUs.
>>>>
>>>> The resulting trajectories of the two runs, however, were identical,
>>>> although different random seeds were used.
>>>>
>>>> Is the ig-seed not used on GPUs, or for NTT=1 in general?
>>>>
>>>> Maybe I misunderstood the section 21.6.7 in the Amber manual about
>>>> temperature regulation...
>>>> I did not check ig=-1 up to now, though.
>>>>
>>>> Best regards,
>>>>
>>>> Anselm
>>>>
>>>> Bioinformatik | NHR.FAU
>>>> Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
>>>> Germany
>>>>
>>>>
>>>>
>>>>
>>>>
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Received on Fri Feb 04 2022 - 09:30:04 PST
