Accelerated molecular dynamics: Energy value in output file

From: Kapil jain (noxtreme007_at_gmail.com)
Date: Tue Aug 19 2014 - 23:53:20 CDT

Hi,

I'm performing aMD (dual boost and dihedral) on membrane protein after 100
ns cMD. The script is as follows

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

# aMD

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

structure al1b_popcwi.psf
coordinates 10000.pdb
outputName amd-boost-1

set temperature 310

# Continuing a job from the restart files
if {0} {
set inputname al1b_popcwimineq-02
binCoordinates $inputname.restart.coor
binVelocities $inputname.restart.vel ;# remove the "temperature"
entry if you use this!
extendedSystem $inputname.restart.xsc
}

firsttimestep 0

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

# Input
paraTypeCharmm on
parameters par_all27_prot_lipid.prm

# NOTE: Do not set the initial velocity temperature if you
# have also specified a .vel restart file!
temperature $temperature
zeromomentum yes

# Periodic Boundary Conditions
# NOTE: Do not set the periodic cell basis if you have also
# specified an .xsc restart file!
if {1} {
cellBasisVector1 69.88 0. 0.
cellBasisVector2 0. 68.66 0.
cellBasisVector3 0. 0. 95.36
cellOrigin 0.28 0.29 6.22
}
wrapWater on
wrapAll on

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5

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

#PME (for full-system periodic electrostatics)
if {1} {
PME yes
PMEGridSpacing 1
}

# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen no

# Constant Pressure Control (variable volume)
if {1} {
useGroupPressure yes ;# needed for 2fs steps
useFlexibleCell yes ;# no for water box, yes for membrane
useConstantRatio yes
useConstantArea no ;# no for water box, yes for membrane

langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 200.
langevinPistonDecay 50.
langevinPistonTemp $temperature
}

restartfreq 5000 ;# 1000steps = every 2ps
dcdfreq 5000
xstFreq 5000
outputEnergies 500
outputPressure 500

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

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

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

accelMD on
accelMDdihe on
accelMDE 8865
accelMDalpha 409
accelMDdual on
accelMDTE -58220
accelMDTalpha 9389
accelMDFirstStep 0
accelMDLastStep 0
accelMDOutFreq 5000

#eFieldOn yes
#eField 0 0 -0.155

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

# Minimization
if {0} {
minimize 1000
reinitvels $temperature
}

run 15000000 ;# 25 ns

but in output file, I'm getting half of the total energy (~ -25000) because
of which protein experiences high energy barrier and distorts after few ns.
Is there something wrong with input parameters or anything else which i
should look on to get proper energy term in output file. I shall be
thankful to you.

Kapil Jain

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