From: Hailey Bureau (hailey.bureau_at_gmail.com)
Date: Sun Sep 08 2013 - 17:54:26 CDT
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 : Wed Dec 31 2014 - 23:21:38 CST