non-repeatability NAMD simulations

From: roberte_at_organ.su.se
Date: Tue May 10 2005 - 17:08:30 CDT

--
I've build a cluster of 4 computers with different intel cpu's ( and one amd
1.8GHz) using Clustermatic 5 ...
However when running the same NAMD simulation on the machine (2 processors or on
all 4 ) the results from the simulations differ, even when using the same SEED
number and starting conditions.. Is this a common problem with NAMD, as I have
not encountered it with Charmm ( when running on a itanium cluster)..
The following input configuration file was used : This is an octasaccharide in a
50Å box already minimized and heated but not fully equilibrated.
Has any one else encountered this problem. It would be nice to be able to get
reproducable results.
(this configuration file was run on two cpu's twice, resulting in two different
energy out-puts. They start to drift apart at about step 1000)
-------------------------------------
#Input
structure	p22_wb.psf
coordinates	p22_wb_min_heat_eq_long.coor
#temperature 	300
velocities	p22_wb_min_heat_eq_long.vel
extendedSystem	p22_wb_min_heat_eq_long.xsc
#firsttimestep	100000
#molly		on
#parameters
paraTypeCharmm	on
parameters	/home/rob/NAMD_2.5_Linux-i686/namd-tutorial-files/parm/parmsu_01.prm
exclude		scaled1-4
1-4scaling	1.0
dielectric	1.0
#setting parameters for long-range
switching	on
switchdist	10.0
cutoff		12.0
pairlistDist	15.0
stepspercycle	4
rigidBonds	none
#rigidTolerance 	0.0001
#rigidIterations	100
# Constant Temperature Control
#langevin            on    ;# do langevin dynamics
#langevinDamping     5     ;# damping coefficient (gamma) of 5/ps
#langevinTemp        300
#langevinHydrogen    off    ;# don't couple langevin bath to hydrogens
#PME
PME		on
#PMETolerance	0.00001
PMEGridSizeX        50
PMEGridSizeY        50
PMEGridSizeZ        50
timestep		1.0
fullElectFrequency	2
#
#minimization 	on
outputenergies	250
outputtiming	250
binaryoutput	no
outputname	p22_wb_test5_2proc_a
restartname	p22_wb_test5_2proc_a
restartfreq	100
binaryrestart	yes
DCDfile		p22_wb_test5_2proc_a.dcd
DCDfreq		250
#numsteps	2000	# this is the steps for minimization
outputPressure 	250
#MD protocol Block
seed 		2010
numsteps	2000
#temperature	300
rescaleFreq	40
rescaleTemp	300
useGroupPressure      yes ;# needed for rigidBonds
useFlexibleCell       no
useConstantArea       no
BerendsenPressure	on
BerendsenPressureTarget	1.01325
BerendsenPressureCompressibility	0.0000457
BerendsenPressureRelaxationTime		100
BerendsenPressureFreq			10
#langevinPiston        on
#langevinPistonTarget  1.01325 ;#  in bar -> 1 atm
#langevinPistonPeriod  100.
#langevinPistonDecay   50.
#langevinPistonTemp    300
#Boundrary Conditions
#cellBasisVector1    49.0    0.    0.
#cellBasisVector2     0.   49.0    0.
#cellBasisVector3     0.    0.   49.0
#cellOrigin           0.    0.    0.
#wrapWater	on
wrapAll    	on

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