not that I see, but if you set nstlim smaller and then ntpr=1, you can more
easily check differences in energies and velocities.
On Fri, Feb 4, 2022 at 12:38 PM Dr. Anselm Horn <anselm.horn.fau.de> wrote:
> 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 - 11:00:02 PST
