From: Richard Overstreet (roverst_at_g.clemson.edu)
Date: Mon Nov 14 2016 - 11:29:27 CST
NAMD Users,
I am attempting to model protein adsorption on periodic graphene under
the NPT ensemble in namd with the langevin barostat. I have successfully
run NVT simulations for this system before however the barrostat is
producing high energies during the simulation run (4e6 kcal/mol). After
some testing I have determined graphene combined with the langevin
barostat produces high energies in the simulation. In an attempt to
prevent this I enabled the "useConstantArea" and "ExcludeFromPressure"
options however total energies for this simulation remain high. I
assumed that excluding the graphene atoms from the pressure calculation
would prevent the scaling of those atomic coordinates and using a
flexible cell with a constant area would only scale the PBC box in the Z
dimension but this does not appear to be the case. In each instance the
barostat appears to be compressing the graphene monolayer producing
energies on the order of 4e6-5e6 kcal/mol. Not sure why namd is ignoring
these options unless I am not implementing the barostat correctly. As a
final note the graphene atoms remain fixed during the simulation using
the "fixedAtoms" option. Any advice is appreciated.
Regards,
Richard Overstreet
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure ./insconfig_tip3_autopsf.psf
coordinates ./ins_ads_e.coor
velocities ./ins_ads_e.vel
set itemp 300
set ftemp 300
set outputname ins_ads_p
firsttimestep 0
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters ./graphene_par_all27_prot_na.prm
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 14.0
# Heating parameters
#temperature $itemp
#rescaleFreq 1
#rescaleTemp $ftemp # The value of temperature to be kept after heating
is completed
#Pressure Paramters
langevin on
langevinTemp $ftemp
LangevinPiston on
LangevinPistonTarget 1.01325
LangevinPistonPeriod 200
LangevinPistonDecay 100
LangevinPistonTemp $ftemp
useFlexibleCell yes
useConstantArea yes
# Integrator Parameters
timestep 1.0
rigidBonds all
nonbondedFreq 1
fullElectFrequency 1
stepspercycle 10
# Periodic Boundary Conditions
cellBasisVector1 105.86000229644776 0.0 0.0
cellBasisVector2 0.0 105.98900129127503 0.0
cellBasisVector3 0.0 0.0 204.62000347900391
cellOrigin 48.24700117111206 48.39250075817108 101.60100173950195
wrapAll on
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSpacing 0
#manual grid definition
PMEGridSizeX 108
PMEGridSizeY 108
PMEGridSizeZ 408
# Output
outputName $outputname
restartfreq 500 ;# 500steps = every 1ps
dcdfreq 250
xstFreq 250
outputEnergies 100
#############################################################
## EXTRA PARAMETERS ##
#############################################################
binaryrestart no
binaryoutput no
fixedAtoms on
fixedAtomsFile ./insconfig_tip3_43.300.pdb
fixedAtomsCol B
ExcludeFromPressure on
ExcludeFromPressureFile ./insconfig_tip3_43.300.pdb
ExcludeFromPressureCol B
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
numsteps 1000000 ;# 2ns
################################OUTPUT###############
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY
MISC KINETIC TOTAL TEMP
POTENTIAL TOTAL3 TEMPAVG PRESSURE
GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 0 30168.5163 3769037.4091 1132606.4435
48.6455 -350132.3687 30823.4125 0.0000
0.0000 58745.3058 4671297.3640 282.9142
4612552.0582 4671498.1484 282.9142 -5843.9748
-5844.0621 2295835.6042 -5843.9748 -5844.0621
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