How to make water stay in the Z direction?

From: Yi Lun Lee (ylee45_at_students.tntech.edu)
Date: Wed Aug 08 2018 - 11:26:11 CDT

Hi all,

I set up a system is that molecule in the middle and water on the top and bottom in Z direction,

but after calculate the water only show one side.

My question is that how to make water stay in the top and bottom in Z direction?

This is my input file:

#############################################################
## JOB DESCRIPTION ##
#############################################################

# production stage

#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################

structure binary-c22.psf
coordinates binary-c22.pdb
bincoordinates pre7.restart.coor
binvelocities pre7.restart.vel

set temperature 300
set outputname chtr-1
seed 1095345678
firsttimestep 0

#############################################################
## SIMULATION PARAMETERS ##
#############################################################

# Input
paraTypeCharmm on
parameters par_all36_prot.prm
parameters par_all36_lipid.prm
parameters par_all36_carb.prm
parameters par_all36_cgenff.prm
parameters toppar_water_ions.str
parameters c22.str

#temperature $temperature

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 14

# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 1
stepspercycle 10
zeroMomentum yes

# Constant Temperature Control
tCouple on
tCoupleTemp $temperature

# Periodic Boundary Conditions
cellBasisVector1 43.4792 0. 0.
cellBasisVector2 0. 43.4792 0.
cellBasisVector3 0. 0. 192.5505
cellOrigin 0. 0. 0.

wrapAll on

# PME (for full-system periodic electrostatics)
PME yes
PMEInterpOrder 6
PMETolerance 0.00001
PMEGridSizeX 40
PMEGridSizeY 40
PMEGridSizeZ 190

# Constant Pressure Control (variable volume)
#useGroupPressure yes ;# needed for rigidBonds
#useFlexibleCell no
#useConstantArea yes
#langevinPiston on
#langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 200.
langevinPistonDecay 100.
langevinPistonTemp $temperature

# Output
outputName $outputname
restartfreq 10000
restartsave yes
dcdfreq 2500
xstFreq 2500
outputEnergies 500
outputPressure 500
outputMomenta 500

#############################################################
## EXTRA PARAMETERS ##
#############################################################

############################################################
## EXECUTION SCRIPT ##
#############################################################

# Equilibration at constant P
run 500000

Thank you

YiLun Lee

This archive was generated by hypermail 2.1.6 : Tue Dec 10 2019 - 23:20:04 CST