[gmx-users] Re: gmx-users Digest, Vol 63, Issue 82

Ragnarok sdf fabracht1 at gmail.com
Fri Jul 17 18:34:09 CEST 2009

The problem is that the .tpr file tells me that the monitoring is
being made between all pairs. I want only the pairs aminoacid1-ligand,
aminoacid2-ligand etc and not aminoacid1-aminoacid2. This kind of
monitoring, i.e., between all possible pairs, gives me .edr files that
are 1Gb or more in size. That is a problem since I need to do the same
type of analysis for 61 more complexes.
So, again, I need to monitor only the pairs in which one of the
members is the LIGAND and the other is one of the aminoacids of that
huge list I posted in the energygrps.

> what is not working exactly?
> This should give you as output all the pair interacts and you can
> select the ones you want ... ?!
> On Jul 17, 2009, at 4:23 PM, Ragnarok sdf wrote:
>> I have created an mdp file with 202 groups for monitoring in the
>> energygrps string. Being 201 of these aminoacids which interact with
>> the 202nd which is the ligand. The problem is that I found out that
>> this does not work properly, and also does not work the way I thought
>> it would work. Well, the deal is that I want to monitor each of the
>> pair interactions, i.e., aminoacid1-ligand, aminoacid2-ligand,
>> aminoacid3-ligand etc. Is there a way I can do this with a single mdp
>> file, or should I create 202 different mdp files and -rerun 202 times
>> the same simulation (which sounds just as crazy as the idea i had
>> before)?
>> Here is what I have written for the energygrps:
>> energygrps          =  _S r_29 r_30 r_61 r_63 r_64 r_65 r_66 r_67 r_68
>> r_69 r_70 r_71 r_72 r_73 r_74 r_75 r_76 r_77 r_78 r_79 r_80 r_81 r_82
>> r_83 r_84 r_85 r_86 r_87 r_88 r_92 r_94 r_95 r_96 r_98 r_111 r_112
>> r_113 r_114 r_115 r_116 r_117 r_118 r_119 r_120 r_121 r_122 r_123
>> r_124 r_125 r_126 r_127 r_128 r_129 r_130 r_131 r_132 r_133 r_134
>> r_142 r_143 r_144 r_145 r_146 r_147 r_148 r_149 r_150 r_151 r_152
>> r_154 r_172 r_195 r_196 r_197 r_198 r_199 r_200 r_201 r_202 r_203
>> r_222 r_223 r_224 r_225 r_226 r_227 r_228 r_231 r_232 r_233 r_234
>> r_243 r_246 r_247 r_249 r_250 r_251 r_275 r_277 r_278 r_279 r_280
>> r_281 r_282 r_283 r_284 r_285 r_286 r_287 r_288 r_289 r_290 r_291
>> r_292 r_293 r_294 r_295 r_296 r_297 r_325 r_326 r_327 r_328 r_329
>> r_330 r_331 r_332 r_333 r_334 r_335 r_336 r_337 r_338 r_339 r_340
>> r_341 r_342 r_343 r_344 r_345 r_346 r_354 r_355 r_356 r_357 r_358
>> r_359 r_360 r_361 r_362 r_363 r_364 r_365 r_367 r_368 r_369 r_370
>> r_371 r_378 r_395 r_396 r_397 r_398 r_399 r_401 r_402 r_403 r_424
>> r_426 r_430 r_432 r_433 r_434 r_435 r_438 r_439 r_440 r_441 r_442
>> r_443 r_444 r_445 r_446 r_447 r_448 r_449 r_450 r_451 r_452 r_453
>> r_456 r_458 r_459 r_460 r_461 r_476 r_521 r_536 r_537 r_538 r_539
>> I would like some advice on the matter.
>> Thank you in advance
>> Fabrício Bracht

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