From: Hemanth Haridas (hemanth.h_at_iitgn.ac.in)
Date: Thu Sep 02 2021 - 04:36:46 CDT
Dear Zeynab,
Can you please post the psf and the input file that you used. I have some
experience in setting up and running umbrella sampling simulations using
Drude FF.
On Thu, Sep 2, 2021 at 12:51 PM zeynab hosseini <hosseinizeynab93_at_gmail.com>
wrote:
> Hi Giacomo,
>
> Thank you so much for your reply. Sorry about that but unfortunately I
> couldn't completely understand your prescription. I made 10
> windows centered at 6.7A, 6.8A, 6.9A, 7A, 8A, 9A, 11A, 13A, 15A and 17A.
> The output I already sent is related to window-0 centered at 6.7A. I
> understood to perform standard MD for each replica independently(short
> one)? but what do you mean by setting the centers of harmonic restraints to
> zero? You mean for example for the window-0 I put the center 0 instead of
> 6.7? That would't produce problem?
>
> All the best,
> Zeynab
>
> On Wed, Sep 1, 2021 at 10:01 AM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
>> Hi Zeynab, I've not used yet polarizable models in NAMD, so I don't know
>> specifically where the error arises. Assuming that this is a symptom of an
>> unstable configuration, what I would try to do is doing for each replica a
>> short MD run of 100-1000 steps on your workstation or an interactive node.
>> Start with the centers of the harmonic restraints to zero as you have shown
>> (i.e. test the configuration of the first replica), and then do the same
>> for all other values that will be set by the REUS script, which will modify
>> that center for all other replicas.
>>
>> Giacomo
>>
>> On Wed, Sep 1, 2021 at 6:28 AM zeynab hosseini <
>> hosseinizeynab93_at_gmail.com> wrote:
>>
>>> 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
>>> <https://urldefense.com/v3/__http://dynamicsgmail.google.com__;!!DZ3fjg!rr1eS3jzXnhCzE3epjT3nvhSxHDTpqYVUUEui1CrLsbun9UvEQqaExjXfxLYr-Ns8Q$>
>>> 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
>>>
>>
-- *Hemanth H 18310019* Research Scholar IIT Gandhinagar
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