use colvars to calculate PMFs by umbrella sampling method

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1

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!

2

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 ?

this is not a question that can be answered with a simple yes or no
(unless you want to hear a "obviously no, because it stops with an
error").

first, you need to make sure that your system is properly equilibrated
and can run reliably with the settings you chose w/o using fix
colvars.
second, you need to make sure that when you add a harmonic restraint
as a collective variable, that the system is equilibrated for that
specific restraint applied and you need to do that for every window.
whether this is done or not, is impossible to say from just looking at
two input files, but you yourself can easily check it out and correct
it, if needed.

axel.