Hello
I utilize colvars module in LAMMPS to calculate PMFs. In this process, I use umbrella sampling method.
My colvars configuration file is:
[[[[
colvarsTrajFrequency 100
colvarsRestartFrequency 1000
colvar {
name bond
width 0.25
lowerBoundary 24.0
upperBoundary 26.0
lowerWallConstant 30.0
upperWallConstant 30.0
distance {
group1 {
atomNumbersRange 43-80
}
group2 {
atomNumbersRange 142-179
}
forceNoPBC yes
}
}
harmonic {
colvars bond
# outputEnergy yes
centers 25.00
forceConstant 100.0
# targetCenters 20.00
# targetNumSteps 100000
# outputCenters yes
# outputAccumulatedWork yes
}
**#**histogram {
# colvars one
# }
]]]
and lammps input configuration file is:
[[[
units real
atom_style full
pair_style lj/cut/coul/long 10.0 15.0
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
improper_style cvff
kspace_style ewald 0.00001
dielectric 1.0
boundary p p p
read_data c2_a_02_water.lammps05
neighbor 2.0 bin
neigh_modify delay 5
timestep 1.0
thermo_style multi
thermo 100
#fix 1 all shake 0.0001 10 10000 b 22 a 44
fix 2 all nvt temp 300.0 300.0 100.0
fix 3 all colvars configuration output c2_02_12
dump 4 all atom 100 dumpves.lammpstrj
dump_modify 4 image yes
restart 1000 tmp.restart
run 10000
]]]
use 12 cores and an error occurred:
ERROR on proc 9: Bond atoms 184 185 missing on proc 9 at step 10 (neigh_bond.cpp:55)
My goal is to acquire the PMFs in a series of constructions with different distance between group1 and group2.
So my lammps configuration file and colvars configuration file is correct or not ?
Thanks!