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

# Minimization and Equilibration of decrosin
# In a water box.  The mdrun for nvt

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

structure          dec-nos3.psf
coordinates        dec-nos3.pdb
outputName         dec_md1

set temperature    310

# Continuing a job from the restart files
if {1} {
set inputname      dec_heat
binCoordinates     $inputname.restart.coor
binVelocities      $inputname.restart.vel ;# remove the "temperature" entry if you use this!
extendedSystem    $inputname.xsc
}

firsttimestep      0

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

# Param Input
paraTypeCharmm     on
parameters          par_all27_prot_lipid.inp

# NOTE: Do not set the initial velocity temperature if you
# have also specified a .vel restart file!
# temperature         $temperature
 
#  GBIS parameters
GBIS                 on
ionConcentration     0.1
alphaCutoff          14
solventDielectric    78.5
intrinsicRadiusOffset 0.09

# Periodic Boundary conditions
# NOTE: Do not set the periodic cell basis if you have also
# specified an .xsc restart file!
if {0} {
cellBasisVector1    52.    0.   0.
cellBasisVector2     0.   47.   0.
cellBasisVector3     0.    0   49.
cellOrigin          3.5  -0.5  -1.9
}
wrapWater           on
wrapAll             on

# Force-Field Parameters
exclude             scaled1-4
1-4scaling          1.0
cutoff              16.0
switching           on
switchdist          15.0
pairlistdist        17.5
# margin              5

# Integrator Parameters
timestep            1.0  ;# 1fs/step
rigidBonds          all  ;# needed for 2fs steps
nonbondedFreq       2
fullElectFrequency  4 
stepspercycle       12

#PME (for full-system periodic electrostatics)
if {0} {
PME                 yes
# PMEGridSizeX        80
# PMEGridSizeY        80
# PMEGridSizeZ        60
PMEGridSpacing      1.0
}

# Constant Temperature Control
langevin            on    ;# do langevin dynamics
langevinDamping     5     ;# damping coefficient (gamma) of 5/ps
langevinTemp        $temperature
langevinHydrogen    no    ;# don't couple langevin bath to hydrogens

# Constant Pressure Control (variable volume)
if {0} {
useGroupPressure      yes ;# needed for 2fs steps
useFlexibleCell       no  ;# no for water box, yes for membrane
useConstantArea       no  ;# no for water box, yes for membrane

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

 

# Fixed Atoms Constraint (set PDB beta-column to 1)
if {0} {
fixedAtoms          on
fixedAtomsFile      dec-2238_wi.pdb
fixedAtomsCol       B
}

# Harmonic restraint parameters
if {0} {
constraints         on
consexp             2
consref             cfd_wi.cstr
conskfile           cfd_wi.cstr
conskcol            B
}

# IMD Settings (can view sim in VMD)
if {0} {
IMDon           on
IMDport         3000    ;# port number (enter it in VMD)
IMDfreq         1       ;# send every 1 frame
IMDwait         no      ;# wait for VMD to connect before running?
}

# Output Freq.
restartfreq         6000     ;# 1000steps = every 1ps
dcdfreq             6000
xstFreq             6000
outputEnergies      1200
outputPressure      1200

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

# Put here any custom parameters that are specific to
# this job (e.g., SMD, TclForces, etc...)

 

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

run 60000000 ;# 60ns

pdb，psf，不加水不加离子

# Force-Field Parameters
cutoff              16.0
switchdist          15.0
pairlistdist        17.5

无PME PBC，NVT进行md

速度大概为含水md的四倍