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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--
Dr. Adrian E. Roitberg (he/him/el)
V.T. and Louise Jackson Professor in Chemistry
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Fri Feb 04 2022 - 09:30:03 PST
