Unable to open binary file md_equ_300.out.rst.vel

From: İmren Bayıl (ib57001_at_student.gaziantep.edu.tr)
Date: Sat Feb 05 2022 - 04:09:31 CST

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 I used amber force field in namd and I finished minimization and
equilibration steps successfully but the last step for run I am getting
this error. Until md run step,I didnt get any error.I did minimization and
equilibration

Unable to open binary file md_equ_300.out.rst.vel

in my working directory;
 namd2
step3_input.parm7
step3_input.rst7
md_equ_300_out.pdb
md_equ_300_out.rst.coor
md_equ_300_out.rst.xsc
md_equ_300_out.rst.vel
job.log
FFTW_NAMD_2.13_Linux-x86_64-multicore.txt
water.namd

also I added water.namd file as attached.

#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

#==========================================================
#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 60000000
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 -116.645 0.0 0.0
#cellBasisVector2 0.0 -116.484 0.0
#cellBasisVector3 0.0 0.0 116.506
#cellOrigin 58.035 57.898 58.181

#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 120
PMEGridSizeY 120
PMEGridSizeZ 120
#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 min_all_out.coor
#fixedAtomsCol O

• application/octet-stream attachment: water.namd

• Next message: Francesco Pietra: "Puzzle with "small molecule" ligand structure in nucleotide environments"
• Previous message: Nicholus Bhattacharjee: "Steered molecular dynamics simulations of peptide with non standard amino acid using GAFF parameter"
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