protein shifts out of the water box

From: Eric Userlist (eric.userlist_at_gmail.com)
Date: Wed Apr 29 2009 - 18:52:16 CDT

Hi
I am running a md simulation with the following input file. After I examine
the trajectory, part of the protein is outside the water grid. I solvate
the protein with 9 angstrom from the edge of the grid. Should I use a bigger
water box or restrain the protein somehow. Thank you.

Eric

###### Input Files and Parameters #######

set temperature 310
set outputname protein_md2
set restartfreq 500

structure ../common/protein_ionized.psf
coordinates ../md/protein_md.pdb
bincoordinates ../md/protein_md.restart.coor
binvelocities ../md/protein_md.restart.vel
extendedSystem ../md/protein_md.xsc

######################
# Force-Field Parameters
paratypecharmm on
parameters ../common/par_all27_prot_lipid.inp
exclude scaled1-4
1-4scaling 1.0
cutoff 9.
switching on
switchdist 8.
pairlistdist 11

# Integrator Parameters
timestep 1.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
rigidTolerance 0.00000001
margin 2.5
nonbondedFreq 2
fullElectFrequency 4
stepspercycle 20

# Temperature Control
langevin on
langevinTemp 310
langevinDamping 1
#temperature $temperature
#reassignFreq 100
#reassignTemp 25
#reassignIncr 25
#reassignHold 300

# Periodic Boundary Conditions
cellBasisVector1 66.3 0 0
cellBasisVector2 0 71.5 0
cellBasisVector3 0 0 78.9
cellOrigin 23.77 24.54 11.70
wrapAll on
wrapNearest on

# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 72
PMEGridSizeY 72
PMEGridSizeZ 80

# Constant Pressure Control (variable volume)
useGroupPressure yes
useFlexibleCell no
LangevinPiston on
LangevinPistonTarget 1
LangevinPistonPeriod 200
LangevinPistonDecay 500
LangevinPistonTemp 310

# Output
outputname $outputname
outputEnergies 10
restartfreq $restartfreq
DCDfreq 500
binaryoutput no
binaryrestart yes
outputTiming 100

########## Extra Parameters ################

# Constraints
#constraints on
#consref ../min/protein_min.pdb
#conskfile ../min/protein_min_constraint.pdb
#conskcol B

########## Execution ##############

#minimize 1000

run 10000000

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