Hello,
I am trying to calculate the potential mean force of a ethanol molecule to enter a polymer membrane.The system has ethanol and water mixture and PIM-1 polymer membrane. I did the minimization , swelling simulation ( nvt with 1 bar pressure) for 10 ns, after that 2ns Npt simulation.All the simulation ran perfectly. Then I am trying to calculate the pmf in npt simulation with using the colvars. However, I am getting the error:
ERROR on proc 0: Bond atoms 26311 26313 missing on proc 0 at step 468 (src/ntopo_bond_partial.cpp:60)
As far I understand when I applying the biasing force, the simulation become unstable even the biasing force I am trying is very small. Could you please suggest anything,how I might try to solve the problem?
For colvars script, I have select one ethanol molecule and 30 polymer molecules which are close to the center of mass of the polymer. Please let me know if I am doing it wrong.
Here is my input script:
colvars script
colvar {
name dist
width 0.1 # Spacing of grids
lowerBoundary -120 #window 1
upperBoundary 40 #window 1
hardLowerBoundary yes
hardUpperBoundary yes
outputAppliedForce on
distanceZ {
axis (0.0, 0.0, 1.0) #Ensure the projection of distance vector on z axis
main {
atomNumbersRange 15310-15318
}
ref {
atomNumbers 3704 3702 5582 5511 5517 5632 5583 3713 3761 5519 5520 5580 5643 5581 5518 5521 5579 5522 5510 5578 3762 5642 5645 5641 5523 3760 5512 5524 5514 5525
}
}
}
harmonic {
name pmf_pot
colvars dist
forceConstant 0.0001
centers -100
targetCenters -80
targetNumStages 20
targetNumSteps 50000
outputCenters yes
}
Input script
System------------------------------------------------------------------------------------
units real
atom_style full
dimension 3
newton on
boundary p p p
timestep 1
Styles--------------------------------------------------------------------------------------
read_data NPT_2ns.data
bond_style hybrid harmonic
angle_style hybrid harmonic
dihedral_style hybrid harmonic opls
improper_style none
pair_style hybrid lj/charmm/coul/long 9.0 12.0 12.0 tersoff
include System_ethanol_water_coeff.in
special_bonds amber
kspace_style pppm 0.00001
#Define group and region -------------------------------------------------------------------
#spearate the polymer & water group
group wall type 12
group ethanol type 13 14 15 16 17 19
group water type 18 20
group polymer type 1 2 3 4 5 6 7 8 9 10 11
group wall1 id 6791:7934
group wall2 id 7935:9078
region membrane block -2.8255 51.1745 -1.558001 52.441999 -70 5 units box
region left_block block -2.8255 51.1745 -1.558001 52.441999 -118 -70 units box
region right_block block -2.8255 51.1745 -1.558001 52.441999 5 40 units box
group Left_block region left_block
group Right_block region right_block
group Membrane region membrane
neigh_modify every 1 delay 0 check yes
#system_specific_setting-------------------------------------------------------------------------
fix fshake water shake 0.000001 2000 0 b 22 a 36
fix makestable wall setforce 0.0 0.0 0.0
fix polymerstable polymer setforce NULL NULL 0.0
fix 1 all npt temp 300.0 300.0 100.0 z 1.0 1.0 500.0
fix mtd all colvars abf.colvars.inp seed 2122
thermo_style custom step temp vol
thermo 1000
run 500000