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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