DMPC Atoms moving too fast !

From: mustapha.hamdi_at_ensi-bourges.fr
Date: Sat Mar 10 2007 - 10:08:08 CST

Dear all

 Thanks Arneh for your suggestions, I was trying simulating the DMPC
membrane with namd, I minimized my system "without water" for 10 000
steps, I ignored the minmization warning:

GRADIENT TOLERANCE: 8.71786e+009
Warning: Bad global exclusion count, possible error!
Warning: Increasing cutoff during minimization may avoid this.
ENERGY: 1 8616665.3079 0.0000 0.0000 5002.3817
    -10187.0958 99999999.9999 0.0000 0.0000 0.0000
  99999999.9999 0.0000 99999999.9999 99999999.9999 0.0000

the potential energy of the system is converging during minimization, but
I have had troubles when heating gradually my system using reassignTemp:

"ERROR: Atoms moving too fast; simulation has become unstable."

Heating config file:

# molecular system
set MOL lipids
structure ${MOL}.psf
#coordinates lipids.pdb
# after minimization
set inprot dmpc_min
coordinates dmpc_min.pdb
velocities dmpc_min.vel
extendedSystem dmpc_min.xsc

set outputname ${MOL}_heat
set heat_restart ${MOL}_heat_restart

# force field
paratypecharmm on
parameters par_all27_prot_lipid.inp
exclude scaled1-4
1-4scaling 1.0

wrapAll on

# approximations

switching on
switchdist 10
cutoff 12
pairlistdist 13.5
margin 5
# center-of-mass motion is automatically removed.

# integrator
#rigidbonds all
timestep 1.0 # in fs.
stepspercycle 20
nonbondedFreq 2 # BerendsenPressureFreq takes this value.

langevinPiston on
langevinPistonTarget 1.01325
langevinPistonPeriod 200
langevinPistonDecay 500
langevinPistonTemp 300

# output
outputName $outputname

dcdfreq 100 ;# how often we output trajectories
xstFreq 100
outputEnergies 100
outputPressure 100
outputtiming 100
binaryoutput no

# for restarting:
restartname $heat_restart
restartfreq 1000
restartsave yes
binaryrestart no ;# preserves more accuracy.

#temperature 0 # sets initial temperature. use '; #' aft "run".
# disable 'temperature' when using a velocity file.

# For heating, use temperature reassignment.
reassignFreq 300 # tuned to be suit 'natural' heating for system.
reassignTemp 0 # to start from 0 Kelvin, else always lagging by 25K.
reassignIncr 25
reassignHold 300

run 50000

---
pdb: http://perso.ensi-bourges.fr/hamdi/Telechargement/lipids.pdb
--
Mustapha Hamdi
PhD Student
Laboratoire Vision et Robotique
ENSI Bourges, France
Tèl: + 33 2 48 48 40 59
WebSite: http://perso.ensi-bourges.fr/hamdi/

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