From: İmren Bayıl (ib57001_at_student.gaziantep.edu.tr)
Date: Fri Jul 22 2022 - 16:49:56 CDT
my calculation has been terminated by system.I want to continue md
simulation from last numps steps.I have tried rearrange my config file but
I couldnt .I attached my namd config file.please somebody help me to which
part I have to change my config file in order to continue my md simulation ?
Thanks
my config file for run md simulation below :
#**********************************************************
# MD complex, Legavine
# namd2 input > output &
# charmrun /usr/local/bin/namd2 ++local +p4 water_equ.namd >
water_equ.namd.out
#**********************************************************
#set inpname md_01_inp
#set outname md_01_out
#==========================================================
# initial config
cwd ./
#velocities
#temperature 310K
#during reading a restart
#firsttimestep 15000
#==========================================================
# input
parmfile step3_input.parm7
ambercoor step3_input.rst7
amber on
readexclusions yes
#coordinates 2O3M_1.pdb
#paraTypeCharmm on
#parameters par_all27_na.prm
#==========================================================
#from restart files
binCoordinates md_equ_300_out.rst.coor
binVelocities md_equ_300_out.rst.vel # uncomment only if temp. if
off
ExtendedSystem md_equ_300_out.rst.xsc
#==========================================================
# output params
outputname md_01.pdb
## or use $outname
binaryoutput no
restartname md_01.rst
## or use $outname.restart
restartfreq 2000
restartsave no
DCDfile md_01.dcd
## or use $outname.dcd
DCDfreq 2000
outputPressure 2000
#==========================================================
# dyanmics params
timestep 2.0
numsteps 50000000
nonbondedFreq 1
#==========================================================
#SHAKE H
rigidBonds all
rigidIterations 500
#==========================================================
# Force field params
exclude scaled1-4
1-4scaling 0.833333
cutoff 14
switching On
switchdist 12
pairlistdist 16
margin 1.0
#==========================================================
# PME (for full-system periodic electrostatics)
PME yes
#PMEInterpOrder 6
PMEGridSizeX 120
PMEGridSizeY 120
PMEGridSizeZ 120
#these values are multiple of 4 and are taken from PBC vector
#==========================================================
## Temperature control Berendsen
#tCouple on
#tCoupleTemp 310K
#tCoupleFile HTpep_couple.pdb
#tCoupleCol B
#==========================================================
## Constant Pressure Control (variable volume)
#useGroupPressure yes
## needed for rigidBonds
#useFlexibleCell no
#useConstantArea no
#==========================================================
##langevinPiston on
#langevinPistonTarget 1.01325
## in bar -> 1 atm
#langevinPistonPeriod 100.
#langevinPistonDecay 50.
#langevinPistonTemp 310
#==========================================================
langevin on # do langevin dynamics
langevinTemp 310
langevinDamping 5 # damping coefficient (gamma) of 1-5/ps
langevinHydrogen off
useFlexibleCell no
langevinPiston on
langevinPistonTarget 1.01325 # in bar -> 1 atm
langevinPistonPeriod 100
langevinPistonDecay 50
langevinPistonTemp 310
#==========================================================
# Periodic Boundary Conditions
#cellBasisVector1 -126.0 0.0 0.0
#cellBasisVector2 0.0 -138.0 0.0
#cellBasisVector3 0.0 0.0 -145.0
#cellOrigin 64.67230224609375 70.6960220336914 74.10343170166016
#take these values from vmd *.prmtop *.rst.coor by calling
#set t [atomselect top all]
#measure minmax $t
#measure center $t
#vecsub{min}{max}
#==========================================================
wrapAll on
wrapwater on
wrapNearest on
#==========================================================
outputEnergies 500
# 100 steps = every 0.2 ps
outputTiming 500
#==========================================================
#fixed atoms
fixedAtoms off
#fixedAtoms on
#fixedAtomsFile min_all_out.coor
#fixedAtomsCol O
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