SWM4 water model simulation

From: saman amiri (saman_amiri00_at_yahoo.com)
Date: Mon Jun 27 2011 - 12:27:34 CDT

Hi all,

I am goingt to simulate SWM4 water molecules using drude polarizable force field. Unfortunately after minimization it is crashed. The following error is presented:

FATAL ERROR: Low global exclusion count!  System unstable or pairlistdist or cutoff too small. 

Increasing cutoff and/or pairlistdist is not helpful. On the other hand, looking at trajectories indicates that during minimization, water molecules would like to break and form some chemical bonds which is so strange.

Would it be possible to look at CONF file (see bellow) and let me know what is the problem?

structure          ../swm4_drude.xplor.psf
coordinates        ../swm4_drude.pdb
outputName            swm4_drude-1

set temperature    248

firsttimestep      0

# Input
paraTypeCharmm        on
drude                         on
parameters          toppar_drude_master_c36a1.STR
drudeTemp           1

temperature         $temperature
 

if {1} {
cellBasisVector1    25.80   0.       0.
cellBasisVector2     0.    25.80     0.
cellBasisVector3     0.     0.      25.80
cellOrigin          -0.05   0.05     0.08
}
wrapWater           on
wrapAll             on

COMmotion  no

# Force-Field Parameters
exclude             scaled1-4
1-4scaling          1.0
cutoff                 10.
switching           on
switchdist          8.
pairlistdist         12.

# Integrator Parameters
timestep            1.0  ;# 1fs/step
rigidBonds          all  ;# needed for 2fs steps
nonbondedFreq       1
fullElectFrequency  2 
stepspercycle       10

#PME (for full-system periodic electrostatics)
PME                 yes
PMEGridSizeX        27
PMEGridSizeY        27
PMEGridSizeZ        27

# Constant Temperature Control
langevin                 on  
langevinDamping     5   
langevinTemp        $temperature
langevinHydrogen    off 

# Constant Pressure Control (variable volume)
useGroupPressure      yes
useFlexibleCell          no
useConstantArea       no 

langevinPiston        on
langevinPistonTarget  1.01325 ;#  in bar -> 1 atm
langevinPistonPeriod  100.
langevinPistonDecay   50.
langevinPistonTemp    $temperature

restartfreq         1000   
dcdfreq             100
xstFreq             1000
outputEnergies      1000
outputPressure      1000

# Minimization
if {1} {minimize            5000
reinitvels          $temperature
}

run 100000

thanks,
Saman

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