From: zeynab hosseini (hosseinizeynab93_at_gmail.com)
Date: Fri Oct 16 2020 - 03:44:27 CDT
Dear All,
I'm interested in calculating the amino acid (AA) adsorption free energy on
the infinite carbon nanotube (CNT) using well-tempered metadynamics
(WTMD). I solvated the CNT+AA system in a water box and let the system
equilibrated (minimization+NPT+ 6ns NVT). Everything is OK with the
standard NVT, but as soon as the WTMD is turned on the water
molecules start to expand in the way that the water box deforms and the
system becomes unstable. The collective variable is the radial distance of
carbon alpha of AA from CNT mass center. I followed the NAMD tutorial to
set up the WTMD parameters. Would be thankful if you guide me what is
wrong.
The NAMD version is 2.13b1. Sometimes, the simulation crashes with the
following message too. But playing with the values of "hillWeight" and
"width" would remove the error although the water molecules are still
expanding:
Warning: Low global exclusion count! (9467 vs 10214) System unstable or
pairlistdist or cutoff too small.
##############################
meta.namd:
# NAMD Config file
# input
coordinates = solvate.pdb
structure = solvate.psf
outputname = cnt-ser_meta_1
paraTypeCharmm on
parameters toppar_c36_jul20/par_all36_prot.prm
mergeCrossterms yes
parameters toppar_c36_jul20/par_all36_lipid.prm
parameters toppar_c36_jul20/par_all36_carb.prm
parameters toppar_c36_jul20/par_all36_na.prm
parameters toppar_c36_jul20/par_all36_cgenff.prm
parameters toppar_c36_jul20/toppar_water_ions-cmt.str
# output
restartfreq 1000 # 1000steps = every 2ps
dcdfreq 1000
xstFreq 1000
outputEnergies 1000
outputPressure 1000
# Continuing a job from the restart files
if {1} {
set inputname cnt-ser_NVT_6
binCoordinates $inputname.restart.coor
binVelocities $inputname.restart.vel # remove the "temperature" entry
if you use this!
extendedSystem $inputname.restart.xsc
}
# Basic dynamics
exclude scaled1-4
1-4scaling 1
# Simulation space partitioning
switching on
switchdist 10
cutoff 12
pairlistdist 13.5
# Multiple timestepping
rigidBonds all
firsttimestep 0
timestep 1
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 20
PME yes
PMEGridSpacing 1.0
# Temperature control
set temperature 310
#temperature $temperature
langevin on
langevinTemp $temperature
langevinDamping 1
langevinHydrogen no
# Pressure Control for NPT Ensemble
useFlexibleCell no
langevinPiston off
#metadynamics
colvars on
colvarsConfig input.in
run 200000
####################################
input.in:
colvarsTrajFrequency 500
colvarsRestartFrequency 1000
colvar {
name Translocation
lowerboundary 4.5
upperboundary 30.5
width 0.5
distanceXY {
main {
atomnumbers { 165 }
}
ref {
atomnumbers {
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28
29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53
54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78
79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102
103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121
122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140
141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159
160
}
}
axis ( 0.0, 0.0, 1.0 )
}
}
metadynamics {
name meta-distance
colvars Translocation
hillWeight 0.1
newHillFrequency 500
dumpFreeEnergyFile yes
writeHillsTrajectory on
hillwidth 0.5
wellTempered on
biasTemperature 1550
}
############################
All the best,
Zeynab
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