From: zeynab hosseini (hosseinizeynab93_at_gmail.com)
Date: Wed Sep 01 2021 - 05:20:30 CDT
Dear All,
I want to perform a replica-exchange umbrella sampling (reUS) on a system
composed of a nanotube and an amino acid solvated in water using a
polarizable force field (Drude). I did the standard MD of the system with
no problem using NAMD 2.14. The collective variable for my system is the
radial distance of the mass center of amino acid from the mass center of
the carbon nanotube. Collective variable is divided by 10 windows. As soon
as, I perform the reUS simulation I get the following error:
colvars: Collective variables biases initialized, 2 in total.
colvars:
----------------------------------------------------------------------
colvars: Collective variables module (re)initialized.
colvars:
----------------------------------------------------------------------
colvars: Updating NAMD interface:
colvars: updating atomic data (0 atoms).
colvars: updating group data (2 scalable groups, 344 atoms in total).
colvars: updating grid object data (0 grid objects in total).
colvars: Re-initialized atom group for variable "Translocation":0/0. 24
atoms: total mass = 154.105, total charge = -0.279001.
colvars: Re-initialized atom group for variable "Translocation":0/1. 320
atoms: total mass = 1921.76, total charge = 5.91999.
colvars: The final output state file will be
"output/0/win-out.job0.0.colvars.state".
colvars: Opening trajectory file "output/0/win-out.job0.0.colvars.traj".
colvars: Redefining the Tcl "cv" command to the new script interface.
Info: Startup phase 13 took 0.00555027 s, 66.3516 MB of memory in use
Info: Startup phase 14 took 5.4094e-05 s, 66.3516 MB of memory in use
Info: Startup phase 15 took 4.1293e-05 s, 67.6719 MB of memory in use
Info: Finished startup at 26.3569 s, 67.6719 MB of memory in use
colvars: # centers = { 6.7 }
colvars: # forceConstant = 0.025 [default]
TCL: Running for 1000 steps
colvars: Updating NAMD interface:
colvars: updating atomic data (0 atoms).
colvars: updating group data (2 scalable groups, 344 atoms in total).
colvars: updating grid object data (0 grid objects in total).
colvars: Re-initialized atom group for variable "Translocation":0/0. 24
atoms: total mass = 154.105, total charge = -0.279001.
colvars: Re-initialized atom group for variable "Translocation":0/1. 320
atoms: total mass = 1921.76, total charge = 5.91999.
colvars: The final output state file will be
"output/0/win-out.job0.0.colvars.state".
FATAL ERROR: Bad global Thole count! (0 vs 707)
FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html
[Partition 0][Node 0] End of program
I have to say that the collective variable is considered to be the mass
center of a group of atoms with no lone-pair. Since the lone-pairs are
massless.
Here is the collective variable conformation file (US-base.in):
colvarsTrajFrequency 100
colvar {
name Translocation
width 0.1
lowerboundary 4.5
upperboundary 18.8
lowerwall 6.5
upperwall 16.8
lowerwallconstant 100.0
upperwallconstant 100.0
distanceXY {
main {
atomnumbers {1 2 6 7 9 10 11 12 13 14 19 20 23 24 25 26 28 29 31
32 34 35 37 38 }
}
ref {
atomnumbers {
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
150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168
169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187
188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206
207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225
226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244
245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263
264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282
283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301
302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320
321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339
340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358
359 360}
}
axis ( 0.0, 0.0, 1.0 )
}
}
harmonic {
name Z
colvars Translocation
centers 0.0
forceConstant 0.025;# 2.5 * 0.1^2 = 0.025
}
Here is the NAMD configuration file to run the simulation:
structure input/rm-bonds-modified.psf
###coordinates input/start%d.pdb
paraTypeCharmm on
parameters toppar_drude/toppar_drude_master_protein_2019g.str;
parameters toppar_drude/toppar_drude_lipid_2017c.str;
parameters toppar_drude/toppar_drude_model_2019g.str;
parameters toppar_drude/toppar_drude_carbohydrate_2019a.str;
parameters toppar_drude/toppar_drude_nucleic_acid_2017c.str;
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
##vdwForceSwitching on
switchdist 10.
pairlistdist 13.5
# Integrator Parameters
timestep 1.0 ;# 1fs/step (only if needed to finish quickly)
#rigidBonds water
nonbondedFreq 2
fullElectFrequency 4
stepspercycle 20
# Constant Temperature Control
langevin on ;# do langevin dynamicsgmail.google.com
langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# Periodic Boundary Conditions
#cellBasisVector1 61.5 0. 0.
#cellBasisVector2 0. 61.5 0.
#cellBasisVector3 0. 0 71.5
#cellOrigin -16.06 -14.75 -12
#wrapAll on
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSpacing 1.0
# Constant Pressure Control (variable volume)
useGroupPressure yes
useConstantArea yes
useFlexibleCell yes
margin 5
Would be very much grateful if somebody could guide me..
All the best,
Zeynab
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