Hello,
I am trying to create an index file to get interaction energies between
hexane (C6H14, 20atoms) molecules (interaction energy between two hexane
molecules) I have 125 hexane molecules in my system. Please help me figure
out what the problem is.
make_ndx -f Hexane-Stack125.gro -o index.ndx
what I get from this command line is:
************************************************
Reading structure file
Going to read 0 old index file(s)
Analysing residue names:
Opening library file /chem_soft/gromacs/share/gromacs/top/aminoacids.dat
There are: 125 OTHER residues
There are: 0 PROTEIN residues
There are: 0 DNA residues
Analysing Other...
0 System : 2500 atoms
1 HEX : 2500 atoms
nr : group ! 'name' nr name 'splitch' nr Enter: list groups
'a': atom & 'del' nr 'splitres' nr 'l': list residues
't': atom type | 'keep' nr 'splitat' nr 'h': help
'r': residue 'res' nr 'chain' char
"name": group 'case': case sensitive 'q': save and quit
**********************************************************************************
1- Can you please help me understand what these mean? I just typed in "q"
and exit.
Then I typed in :
grompp -f em18.mdp -c Hexane-Stack125.gro -n index.ndx -p
Hexane-Stack125.top -o input.tpr and I got:
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa.itp
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaanb.itp
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaabon.itp
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Hexane'
turning all bonds into constraints...
processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
initialising group options...
processing index file...
Making dummy/rest group for T-Coupling containing 2500 elements
Making dummy/rest group for Acceleration containing 2500 elements
Making dummy/rest group for Freeze containing 2500 elements
-------------------------------------------------------
Program grompp, VERSION 4.0.7
Source code file: readir.c, line: 1007
Fatal error:
Group Hexane not found in indexfile.
Maybe you have non-default goups in your mdp file, while not using the '-n'
option of grompp.
In that case use the '-n' option.
-------------------------------------------------------
mdp file:
title = Hexane
cpp = /lib/cpp
;define = -DFLEX_SPC ; This define statement is completely
irrelevant if you're not dealing with water.
constraints = all-bonds
integrator = steep
dt = 0.002 ; ps !
nsteps = 200
nstlist = 10
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
;
; Energy minimizing stuff
;
emtol = 1000.0
emstep = 0.01
energygrps = Hexane Hexane
index.ndx:
[ System ]
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
151 152 153 154 155 156 157 158 159 160 161 162 163 164 165
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
361 362 363 364 365 366 367 368 369 370 371 372 373 374 375
376 377 378 379 380 381 382 383 384 385 386 387 388 389 390
391 392 393 394 395 396 397 398 399 400 401 402 403 404 405
406 407 408 409 410 411 412 413 414 415 416 417 418 419 420
421 422 423 424 425 426 427 428 429 430 431 432 433 434 435
436 437 438 439 440 441 442 443 444 445 446 447 448 449 450
451 452 453 454 455 456 457 458 459 460 461 462 463 464 465
466 467 468 469 470 471 472 473 474 475 476 477 478 479 480
481 482 483 484 485 486 487 488 489 490 491 492 493 494 495
496 497 498 499 500 501 502 503 504 505 506 507 508 509 510
511 512 513 514 515 516 517 518 519 520 521 522 523 524 525
526 527 528 529 530 531 532 533 534 535 536 537 538 539 540
...
.
.
.
2446 2447 2448 2449 2450 2451 2452 2453 2454 2455 2456 2457 2458 2459 2460
2461 2462 2463 2464 2465 2466 2467 2468 2469 2470 2471 2472 2473 2474 2475
2476 2477 2478 2479 2480 2481 2482 2483 2484 2485 2486 2487 2488 2489 2490
2491 2492 2493 2494 2495 2496 2497 2498 2499 2500
[ HEX
]
***********************************************************2- I have a
question here: why the first group is named [system] and the second Hex?
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
.
.
.
.2341 2342 2343 2344 2345 2346 2347 2348 2349 2350 2351 2352 2353 2354 2355
2356 2357 2358 2359 2360 2361 2362 2363 2364 2365 2366 2367 2368 2369 2370
2371 2372 2373 2374 2375 2376 2377 2378 2379 2380 2381 2382 2383 2384 2385
2386 2387 2388 2389 2390 2391 2392 2393 2394 2395 2396 2397 2398 2399 2400
2401 2402 2403 2404 2405 2406 2407 2408 2409 2410 2411 2412 2413 2414 2415
2416 2417 2418 2419 2420 2421 2422 2423 2424 2425 2426 2427 2428 2429 2430
2431 2432 2433 2434 2435 2436 2437 2438 2439 2440 2441 2442 2443 2444 2445
2446 2447 2448 2449 2450 2451 2452 2453 2454 2455 2456 2457 2458 2459 2460
2461 2462 2463 2464 2465 2466 2467 2468 2469 2470 2471 2472 2473 2474 2475
2476 2477 2478 2479 2480 2481 2482 2483 2484 2485 2486 2487 2488 2489 2490
2491 2492 2493 2494 2495 2496 2497 2498 2499 2500
I though maybe I should change the name in brackets. I renamed [system] an
d{HEX}to {Hexane] . I grompped again:
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa.itp
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaanb.itp
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaabon.itp
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Hexane'
turning all bonds into constraints...
processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
initialising group options...
processing index file...
Making dummy/rest group for T-Coupling containing 2500 elements
Making dummy/rest group for Acceleration containing 2500 elements
Making dummy/rest group for Freeze containing 2500 elements
-------------------------------------------------------
Program grompp, VERSION 4.0.7
Source code file: readir.c, line: 1052
Fatal error:
Atom 1 in multiple Energy Mon. groups (1 and 2)
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