From: Hailey Bureau (hailey.bureau_at_gmail.com)
Date: Mon Sep 09 2013 - 08:07:19 CDT
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. 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
>
>
>
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:23:41 CST