**From:** Axel Kohlmeyer (*akohlmey_at_gmail.com*)

**Date:** Mon Sep 09 2013 - 09:06:19 CDT

**Next message:**James Starlight: "Equilibration of the membrane bilayers with CUDA-support"**Previous message:**JÃ©rÃ´me HÃ©nin: "Re: explicit NVT simulation"**In reply to:**JÃ©rÃ´me HÃ©nin: "Re: explicit NVT simulation"**Next in thread:**Kenno Vanommeslaeghe: "Re: explicit NVT simulation"**Reply:**Kenno Vanommeslaeghe: "Re: explicit NVT simulation"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

On Mon, Sep 9, 2013 at 3:31 PM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:

*> 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).
*

yes, they are forward deterministic, but you cannot reverse the

trajectory and get back to the beginning.

ciao,

axel.

p.s.: it is fun to outnitpick an experienced nitpicker. ;-)

*>
*

*> 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.
*

*>>
*

*>>
*

-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy.

**Next message:**James Starlight: "Equilibration of the membrane bilayers with CUDA-support"**Previous message:**JÃ©rÃ´me HÃ©nin: "Re: explicit NVT simulation"**In reply to:**JÃ©rÃ´me HÃ©nin: "Re: explicit NVT simulation"**Next in thread:**Kenno Vanommeslaeghe: "Re: explicit NVT simulation"**Reply:**Kenno Vanommeslaeghe: "Re: explicit NVT simulation"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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