From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Sep 09 2013 - 08:31:03 CDT
Dear Axel,
If I really want to be an extreme nitpicker - and who doesn't!!! - I must say that together with fixed-point math, you could use a deterministic thermostat or barostat (which I think they all are, as long as the PRNG is and the math is associative).
You're most welcome.
Jérôme
----- Original Message -----
> On Mon, Sep 9, 2013 at 3:07 PM, Hailey Bureau
> <hailey.bureau_at_gmail.com> wrote:
> > Hi Norman,
> >
> > Thanks for your response!
> >
> > I actually am using only one cpu, as I mentioned in my earlier
> > email (granted it isn't the same cpu everytime, in which case I
> > don't know if that would affect the results; perhaps it would).
> > The thing that is keeping me stuck is that I can generate the
> > exact same data using vacuum and implicit solvent conditions, and
> > it seems that only in the case of explicit solvent I am having
> > trouble reproducing data. I am just wondering if there is
> > something specifically going on in only the case of explicit
> > solvent where I cannot reproduce data. However, what's even more
> > puzzling to me is that I can reproduce *some trajectories. For
> > example, between two batches of 5 trajectories each coming from
> > the same 5 seeds, one or two of them will end up identical. The
> > others; however, do not. Any further insight you might have would
> > be greatly appreciated.
>
> if you want perfectly reproducible (and reversible!) trajectories,
> you
> will have to write an MD code that uses fixed point math instead of
> floating point and you must not use any thermostat or barostat.
> floating point math is not associative and thus your trajectories
> will
> sooner or later diverge, since there are certain conditions that will
> trigger the tiniest bit change and from then on you will get
> exponentially diverging trajectories. MD is solving a system of
> linear
> partial differential equations, which exhibits chaotic behavior. of
> course, the more items are involved, the larger the probability of an
> event initiating the divergence.
>
> that being said, whether your trajectories are perfectly reproducible
> has no relevance whether they are correct or not. in fact, often this
> divergence is desirable, as you can quickly produce decorrelated
> trajectories, which allows you to increase phase space sampling
> through concurrent simulations (cf. parallel replica MD). the final
> coordinates of a simulation (in equilibrium) are of little to no
> relevance, averages however are and those should converge to
> consistent results regardless of whether you get diverging
> trajectories or not.
>
> axel.
>
>
> Thanks!
> >
> >
> > -Hailey
> >
> >
> > On Sep 9, 2013, at 2:26 AM, "Norman Geist"
> > <norman.geist_at_uni-greifswald.de> wrote:
> >
> >> Hi Hailey,
> >>
> >> 1st thing to mention is that the parallelization itself can change
> >> results
> >> slightly. This happens due varying orders of arriving part results
> >> that get
> >> computed together. If you changed the number of processors between
> >> the 5
> >> trajectories you mentioned, this could be a 1st likely reason.
> >> Furthermore,
> >> but only an assumption, the load balancer can have additional
> >> impact as
> >> individual core performance can have a random nature and not every
> >> core is
> >> as fast as the others, even if same model. Moreover I'm not sure
> >> if the
> >> langevin thermostat comes with random forces.
> >>
> >> To clarify all these things, try using only a single cpu core for
> >> some
> >> tests. This will eliminate the load balancer and the
> >> parallelization and
> >> will show if other thing in your simulation come with any
> >> randomness.
> >>
> >> Norman Geist.
> >>
> >>
> >>> -----Ursprüngliche Nachricht-----
> >>> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu]
> >>> Im
> >>> Auftrag von Hailey Bureau
> >>> Gesendet: Montag, 9. September 2013 00:54
> >>> An: NAMD list
> >>> Betreff: namd-l: explicit NVT simulation
> >>>
> >>> Hello,
> >>>
> >>> I am running an explicit NVT simulation and I am having trouble
> >>> reproducing data, using the same starting coordinates and random
> >>> seed
> >>> value. In a batch of 5 trajectories, that I run two times with
> >>> identical seed values, I see different results. However,
> >>> sometimes the
> >>> trajectories do turn out the same. I have been trying to find any
> >>> previous interest in this sort of problem and how to solve it,
> >>> but I
> >>> haven't had much luck. Has anyone encountered a problem like this
> >>> before? I am running on one CPU; below is my starting
> >>> configuration
> >>> file:
> >>>
> >>>
> >>> #############################################################
> >>> ## ADJUSTABLE PARAMETERS ##
> >>> #############################################################
> >>> structure ../../../../00.struc/03.exp/00.psf
> >>> coordinates ../../../../00.struc/03.exp/00.pdb
> >>> outputName daOut
> >>> #############################################################
> >>> ## SIMULATION PARAMETERS ##
> >>> #############################################################
> >>> # Input
> >>> seed xxxxx
> >>> paraTypeCharmm on
> >>> parameters ../../../../toppar/par_all27_prot_lipid.prm
> >>> temperature 300
> >>>
> >>> # Force-Field Parameters
> >>> exclude scaled1-4
> >>> 1-4scaling 1.0
> >>> cutoff 12.0
> >>> switching on
> >>> switchdist 10.0
> >>> pairlistdist 13.5
> >>>
> >>> # Integrator Parameters
> >>> timestep 2.0 ;# 2fs/step
> >>> rigidBonds all ;# needed for 2fs steps
> >>> nonbondedFreq 1
> >>> fullElectFrequency 2
> >>> stepspercycle 10
> >>>
> >>> # Constant Temperature Control
> >>> langevin on ;# do langevin dynamics
> >>> langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
> >>> langevinTemp 300
> >>> langevinHydrogen no ;# don't couple langevin bath to
> >>> hydrogens
> >>>
> >>> # Periodic Boundary conditions
> >>> # NOTE: Do not set the periodic cell basis if you have also
> >>> # specified an .xsc restart file!
> >>> if {1} {
> >>> cellBasisVector1 27.0 0.0 0.0
> >>> cellBasisVector2 0.0 24.0 0.0
> >>> cellBasisVector3 0.0 0.0 54.0
> >>> cellOrigin 2.28 -0.35 16.49
> >>> }
> >>> wrapWater on
> >>> wrapAll on
> >>>
> >>> # PME (for full-system periodic electrostatics)
> >>> if {1} {
> >>> PME yes
> >>> #PMEGridSpacing 1.0
> >>> #manual grid definition
> >>> PMEGridSizeX 27
> >>> PMEGridSizeY 24
> >>> PMEGridSizeZ 54
> >>> }
> >>>
> >>> # Constant Pressure Control (variable volume)
> >>> useGroupPressure yes ;# needed for rigidBonds
> >>> useFlexibleCell no
> >>> useConstantArea no
> >>>
> >>> langevinPiston off
> >>> #langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> >>> #langevinPistonPeriod 100.0
> >>> #langevinPistonDecay 50.0
> >>> #langevinPistonTemp 300
> >>>
> >>> # Output
> >>> binaryoutput no
> >>> dcdfreq 100 ;# 500steps = every 1ps
> >>> outputEnergies 500
> >>>
> >>> #############################################################
> >>> ## EXTRA PARAMETERS ##
> >>> #############################################################
> >>> # Tcl interface
> >>> tclForces on
> >>> tclForcesScript smdforce.tcl
> >>>
> >>> run 10000 ;# 20 ps
> >>
> >>
> >>
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
>
>
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