Dear Carlos,
> correcting my typo: if you set tempi>0 (not temp0>0)
> then the seed should
> affect the velocity assignment.
yes, that's what I thought.
I had the following input for this test:
&cntrl
imin = 0,
nstlim = 100000,
dt = 0.002
ntt = 1,
temp0 = 310.0,
tempi = 050.0,
ntp = 1,
ntb = 2,
ntc = 2,
ntf = 2,
ntr = 1,
restraint_wt = 5.0,
restraintmask =':1-100',
ntwx =10000,
ntwe =10000,
ntwr =500000,
ntpr =10000,
ioutfm = 1,
ig = 112233,
&end
Is there obvious mistake?
Best regards,
Anselm
Am 04.02.2022 um 18:21 schrieb Carlos Simmerling:
>
> On Fri, Feb 4, 2022 at 12:11 PM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
>> ntt=1 doesn't use the random number generator, so won't be affected by the
>> seed (ntt=3 is). if you set temp0>0, then the seed should affect the
>> initial velocity assignment.
>>
>> On Fri, Feb 4, 2022 at 12:01 PM Dr. Anselm Horn <anselm.horn.fau.de>
>> wrote:
>>
>>> 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 - 10:00:02 PST
