From: Junwoong Yoon (junwoony_at_andrew.cmu.edu)
Date: Thu Jul 05 2018 - 20:55:29 CDT
Hi all,
I'm doing a simple adsorption energy calculations of a surfactant molecule
onto a hard surface (graphene) in the presence of water molecules (water
box) using ABF (with distanceZ colvar). Le'ts say the original z-direction
coordinate of the surfactant as "z0", Then it only either goes down toward
lowerBoundary or goes up toward upperBoundary. Then the simulation gets
stuck near the boundary and does not explore the other way.
It seems like without solvation box, it worked fine (simulation could
explore the entire range in boundaries). However with the water solvation
box, this thing happens.
Here's what I have been tried but could not resolve this issue:
1) changing the grid limit (lower & upper boundaries)
2) changing original height, z0
3) increasing fullSamples value
Please give me any recommendation if you ever seen this kind of issue
before or have any idea to resolve it.
FYI, I have copied my colvars and namd configuration files here.
######### CONFIG FILE ##########
cellBasisVector1 51.05 0.0 0.0
cellBasisVector2 0.0 51.579 0.0
cellBasisVector3 0.0 0.0 70
cellOrigin 0.0 0.0 0.0
coordinates SDS_graphene_wb.pdb
#extendedSystem SDS_graphene_wb.xst
temperature 300
XSTfile ./output/cntabf
XSTfreq 1000
set temp 300
set numstep 10000000
switching on
switchdist 10
cutoff 12
pairlistdist 14.5
margin 10.0
stepspercycle 20
#wrapWater on
wrapAll on
#useFlexibleCell no
#useConstantArea no
#useGroupPressure no
langevinPiston on
langevinPistonTarget 1.01325
langevinPistonPeriod 200
langevinPistonDecay 100
langevinPistonTemp $temp
langevin on
langevinTemp $temp
langevinDamping 0.5
#This probably isn't necessary
reassignFreq 100000
reassignTemp $temp
PME off
PMEGridSizeX 108
PMEGridSizeY 108
PMEGridSizeZ 80
#Use structures for molecule and a small number of graphene parameters
structure SDS_graphene_wb.psf
paraTypeCharmm on
parameters par_all27_prot_lipid.inp
parameters par_cntgraph.inp
exclude scaled1-4
1-4scaling 1.0
timestep 1.0
#rigidBonds all
fullElectFrequency 4
numsteps $numstep
outputtiming 1000
outputenergies 1000
outputname ./output/cntabf
restartName ./restart/cntabf
restartFreq 1000
fixedAtoms on
fixedAtomsFile SDS_graphene_wb.pdb
DCDfile ./output/cnt_abf.dcd
DCDfreq 1000
colvars on
colvarsConfig colvars_config_custom.tcl
minimize 1000
reinitvels $temp
run $numstep
######### COLVARS FILE ################
colvarsTrajFrequency 1000
colvarsRestartFrequency 1000
smp off
colvar {
name particleZ
width 0.1
lowerboundary 3
upperboundary 30
lowerwallconstant 5
upperwallconstant 5
distanceZ {
#look this up in NAMD user guide
main {
atomsFile SDS_graphene_wb.pdb
atomsCol B
atomsColValue 1
}
ref {
atomsFile SDS_graphene_wb.pdb
atomsCol B
atomsColValue 2
}
}
}
abf {
name densityABF
#timestepfactor 10
colvars particleZ
historyFreq 500
outputFreq 1000
fullSamples 500
}
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