[gmx-users] mdp file for monitoring pair groups

[Justin A. Lemkul]

Ragnarok sdf wrote:
> 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.
> 

Gromacs is working as it should.  I don't believe there is any way to specify an 
"energy pair" as you want it.  To consider 200+ interactions, you have the side 
effect of getting a 200x200 matrix of interactions.

Does your ligand really interact with 200 amino acids, or does it potentially 
interact with 200 amino acids?  If you run the trajectory to see which amino 
acids are actually interacting, you can -rerun with substantially less energy 
groups defined.

-Justin

>> 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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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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