atoms moving fast

From: Xiang Mao (
Date: Sat Sep 08 2007 - 08:31:30 CDT

Hello, everyone:
         I met some problem when I continue my MD. The error message is
atoms moving too fast. After minimize the system, I equilibrated the
system for 100ps, no problem at all, I set temperature to 310, the average
temperature in the equilibrium is about 330K(I think it might be ok). But
when I try to do MD further, the temperature keeps going up. And when it
goes to another 36ps, the MD stop, and got the error message. I have check
the last coordiation of the protein, and that specific atom, all of them are
ok. Attached is my config file. I am wondering if someone could give me some
suggestion about my problem. I really appreciate it.


structure solvate.psf
coordinates pep_wat_eq.coor
velocities pep_wat_eq.vel
extendedSystem pep_wat_eq.xsc
parameters par_all27_prot_lipid_na.inp
paraTypeCharmm on

outputEnergies 1000
outputTiming 1000
xstFreq 1000
dcdFreq 1000
restartfreq 1000
wrapAll on
wrapNearest on

timestep 2
nonBondedFreq 2
fullElectFrequency 4
stepsPerCycle 20

switching on
switchDist 12
cutoff 14
pairlistdist 16

# Periodic Boundary Conditions
cellBasisVector1 75.44 0. 0.
cellBasisVector2 0. 66.46 0.
cellBasisVector3 0. 0 97.63
cellOrigin -21.99 -15.72 -32.98

# the z dimension is going to shrink so pad sufficiently
# the margin could be reduced once the cell is equilibrated
# margin 2

Pme on
PmeGridsizeX 128
PmeGridsizeY 128
PmeGridsizeZ 128

exclude scaled1-4
1-4scaling 1.0
COMmotion no
dielectric 1.0

# use lighter damping now that system is equilibrated
langevin on
langevinDamping 1
langevinTemp 310
langevinHydrogen no

# use lighter damping now that system is equilibrated
langevinPiston on
langevinPistonTarget 1.01325
langevinPistonPeriod 200
langevinPistonDecay 500
langevinPistonTemp 310

useGroupPressure yes
useFlexibleCell no
useConstantRatio no
outputname pep_wat

firsttimestep 50000
run 500000

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