From: İmren Bayıl (ib57001_at_student.gaziantep.edu.tr)
Date: Sat May 21 2022 - 09:38:44 CDT
I want to apply md simulations my dna structure so using tleap I wrote
prmtop and rst7 for my dna structures then I used these two files in namd
.Minimization is running but the output files not occur I dont understand
why? Where is my mistake ? I also attached job.log
#**********************************************************
# Minimization, fix Protein, Legavine
# namd2 input >output &
#
#**********************************************************
#set inpname md_water_inp
#set outname md_water_out
#==========================================================
# initial config
cwd ./
#velocities
temperature 310K
#seed 14988860
#during reading a restart
#firsttimestep ZZZ
#==========================================================
# input
parmfile 3sam_vac.prmtop
ambercoor 3sam_vac.rst7
amber on
readexclusions yes
#==========================================================
#from restart files
binCoordinates min_all_out.rst.coor
#binCoordinates $inpname.rst.coor
#binVelocities $inpname.rst.vel
#ExtendedSystem $inpname.rst.xsc
#==========================================================
# output params
outputname md_water_out.pdb
## or use $outname
binaryoutput no
restartname md_water_out.rst
## or use $outname.restart
restartfreq 1000
restartsave no
DCDfile md_water_out.dcd
## or use $outname.dcd
DCDfreq 500
outputPressure 500
#==========================================================
# dyanmics params
timestep 2.0
numsteps 10000
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
#==========================================================
## 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 -30 0.0 0.0
cellBasisVector2 0.0 -30 0.0
cellBasisVector3 0.0 0.0 -220
cellOrigin 10.161 15.266 109.705
#take these values from vmd *.prmtop *.rst.coor by calling
#set t [atomselect top all]
#measure minmax $t
#measure center $t
#vecsub{min}{max}
#==========================================================
# PME (for full-system periodic electrostatics)
PME yes
#PMEInterpOrder 6
PMEGridSizeX 30
PMEGridSizeY 30
PMEGridSizeZ 225
#these values are multiple of 4 and are taken from PBC vector
#==========================================================
#wrapAll on
wrapwater on
wrapNearest on
#==========================================================v
outputEnergies 500
# 100 steps = every 0.2 ps
outputTiming 500
#==========================================================
#fixed atoms
#fixedAtoms off
fixedAtoms on
fixedAtomsFile fix.pdb # in pdb file 1 means fixed
fixedAtomsCol B
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