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plumed.dat
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plumed.dat
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#SOLUTIONFILE=plumed_TDP-43.dat
MOLINFO MOLTYPE=protein STRUCTURE=input_af.pdb
WHOLEMOLECULES ENTITY0=1-414
distance_rest_domains: CONTACTMAP ...
ATOMS1=1,4
ATOMS2=2,5
ATOMS3=2,20
ATOMS4=28,79
ATOMS5=31,79
ATOMS6=35,79
ATOMS7=37,79
ATOMS8=38,79
ATOMS9=39,79
ATOMS10=40,79
ATOMS11=41,79
ATOMS12=42,79
ATOMS13=74,79
ATOMS14=75,79
ATOMS15=76,79
ATOMS16=102,105
ATOMS17=102,106
ATOMS18=102,150
ATOMS19=102,151
ATOMS20=102,152
ATOMS21=102,155
ATOMS22=102,158
ATOMS23=102,159
ATOMS24=102,161
ATOMS25=103,106
ATOMS26=103,107
ATOMS27=103,108
ATOMS28=103,120
ATOMS29=103,121
ATOMS30=103,124
ATOMS31=103,130
ATOMS32=103,131
ATOMS33=103,132
ATOMS34=103,133
ATOMS35=103,134
ATOMS36=103,135
ATOMS37=103,147
ATOMS38=103,148
ATOMS39=103,149
ATOMS40=103,150
ATOMS41=103,151
ATOMS42=103,152
ATOMS43=103,153
ATOMS44=103,154
ATOMS45=103,155
ATOMS46=103,156
ATOMS47=103,157
ATOMS48=103,158
ATOMS49=103,159
ATOMS50=103,160
ATOMS51=103,161
ATOMS52=103,162
ATOMS53=103,175
ATOMS54=103,176
ATOMS55=103,177
ATOMS56=103,178
ATOMS57=104,178
ATOMS58=105,178
ATOMS59=105,179
ATOMS60=106,178
ATOMS61=106,179
ATOMS62=107,178
ATOMS63=107,179
ATOMS64=108,178
ATOMS65=108,179
ATOMS66=109,178
ATOMS67=109,179
ATOMS68=110,178
ATOMS69=111,178
ATOMS70=120,178
ATOMS71=124,178
ATOMS72=131,178
ATOMS73=132,178
ATOMS74=133,178
ATOMS75=134,178
ATOMS76=135,178
ATOMS77=136,178
ATOMS78=137,178
ATOMS79=145,178
ATOMS80=146,178
ATOMS81=147,178
ATOMS82=147,179
ATOMS83=148,178
ATOMS84=148,179
ATOMS85=149,178
ATOMS86=149,179
ATOMS87=150,178
ATOMS88=150,179
ATOMS89=151,178
ATOMS90=151,179
ATOMS91=152,178
ATOMS92=155,178
ATOMS93=158,178
ATOMS94=159,178
ATOMS95=159,179
ATOMS96=161,178
ATOMS97=161,179
ATOMS98=162,178
ATOMS99=162,179
ATOMS100=163,178
ATOMS101=164,178
ATOMS102=165,178
ATOMS103=166,178
ATOMS104=173,178
ATOMS105=174,178
ATOMS106=174,179
ATOMS107=175,178
ATOMS108=175,179
ATOMS109=176,179
ATOMS110=189,192
ATOMS111=189,233
ATOMS112=189,240
ATOMS113=190,193
ATOMS114=190,194
ATOMS115=190,195
ATOMS116=190,209
ATOMS117=190,210
ATOMS118=190,211
ATOMS119=190,212
ATOMS120=190,213
ATOMS121=190,214
ATOMS122=190,216
ATOMS123=190,217
ATOMS124=190,218
ATOMS125=190,219
ATOMS126=190,220
ATOMS127=190,230
ATOMS128=190,231
ATOMS129=190,232
ATOMS130=190,233
ATOMS131=190,234
ATOMS132=190,235
ATOMS133=190,236
ATOMS134=190,237
ATOMS135=190,238
ATOMS136=190,239
ATOMS137=190,240
ATOMS138=190,241
ATOMS139=190,242
ATOMS140=190,243
ATOMS141=190,244
ATOMS142=190,257
ATOMS143=190,258
ATOMS144=191,260
ATOMS145=192,260
ATOMS146=192,261
ATOMS147=193,260
ATOMS148=193,261
ATOMS149=193,262
ATOMS150=194,260
ATOMS151=194,261
ATOMS152=194,262
ATOMS153=195,260
ATOMS154=195,261
ATOMS155=196,260
ATOMS156=197,260
ATOMS157=211,260
ATOMS158=219,260
ATOMS159=221,260
ATOMS160=222,260
ATOMS161=223,260
ATOMS162=229,260
ATOMS163=229,261
ATOMS164=230,260
ATOMS165=230,261
ATOMS166=231,260
ATOMS167=231,261
ATOMS168=232,260
ATOMS169=232,261
ATOMS170=233,260
ATOMS171=234,260
ATOMS172=234,261
ATOMS173=236,260
ATOMS174=237,260
ATOMS175=238,260
ATOMS176=239,260
ATOMS177=240,260
ATOMS178=241,260
ATOMS179=241,261
ATOMS180=242,260
ATOMS181=243,260
ATOMS182=243,261
ATOMS183=244,260
ATOMS184=245,260
ATOMS185=246,260
ATOMS186=247,260
ATOMS187=248,260
ATOMS188=255,260
ATOMS189=256,260
ATOMS190=256,261
ATOMS191=257,260
ATOMS192=257,261
ATOMS193=258,261
ATOMS194=258,262
ATOMS195=259,262
ATOMS196=298,301
ATOMS197=300,303
ATOMS198=304,307
ATOMS199=318,321
ATOMS200=321,324
ATOMS201=321,325
ATOMS202=321,326
ATOMS203=322,325
ATOMS204=322,326
ATOMS205=323,326
ATOMS206=323,327
ATOMS207=324,327
ATOMS208=325,328
ATOMS209=326,329
ATOMS210=348,351
ATOMS211=350,353
ATOMS212=351,354
ATOMS213=352,355
ATOMS214=357,360
ATOMS215=360,363
ATOMS216=371,374
ATOMS217=376,379
ATOMS218=386,389
ATOMS219=392,395
ATOMS220=394,397
ATOMS221=396,399
ATOMS222=399,402
ATOMS223=400,403
ATOMS224=402,405
ATOMS225=402,406
ATOMS226=407,411
ATOMS227=408,411
SWITCH={CUSTOM FUNC=x R_0=1}
...
af_dist_rest: CONSTANT VALUES=1.0032847926020623,1.0311901761218905,0.7455537494271994,1.7088723132386805,1.713635583035648,1.5095473634079102,1.1722138326615095,1.2549746362492442,0.9444370301440359,1.2123430594801905,1.5226123476400972,1.3369803665205837,1.4350552991032601,1.271596952714026,0.8981292195618154,1.084396699629724,1.2897209025919436,1.5121250515803697,1.0559752460569143,1.0836912801489234,0.707867799885571,0.9799594385549426,1.2259459158405663,1.5500808618962765,0.9052655544131994,1.3762398231774569,1.5152623694390062,1.68192987870425,1.6158358810469509,1.3273277390748264,1.1055688032880424,0.7953455133363603,1.0522321155294776,1.3843332368880512,1.5040866650640965,1.9200282409787175,1.9061048422008757,1.6269824001938105,1.2354281768202782,1.0676583984866739,0.6573523612692953,0.6149551127105952,0.7450687747448683,0.7618590366095304,0.5613296514376999,1.0004315715283156,0.8841317959129811,0.5908093221485615,0.9980626434087752,1.263882938399911,1.1281702172011137,1.1415027465671301,1.3193011650815607,1.4435925820842384,1.1070262966677549,1.31037020906806,0.8523610839620233,0.6740215603262186,1.1396584818139672,0.7467208079993726,1.1898928672075273,0.4552792670205237,0.8395836766809226,1.017876618169248,1.3974865483120085,1.0051763331517576,1.1795675404369834,1.4049736192449929,1.459107712842524,1.5650913815945389,1.59471937045455,1.5574198851361871,1.3527641544118525,1.4486837401986123,1.1706370314583183,1.4376086220145226,1.1653784492984414,1.7256552413105966,1.4055226838216186,1.427379228360951,0.9732663879171014,1.2228183863684539,0.9791120953857901,1.3816555082798005,0.7472525445744396,1.2260105818510056,1.0942220810800791,1.5762166528031232,1.1099413389340045,1.5934589028358461,1.434581000171602,1.630307266302407,1.2566113555803897,1.5485478518530726,1.81100521478802,1.3977122131735087,1.7663343697786331,1.162875016592443,1.430508084408939,1.6525550663471222,1.7831156572327018,1.785999870300293,1.6451806398108602,1.4654783833771945,1.2249537132680417,1.3939366523176433,1.0378110969439147,1.3681153113022448,0.9096965923905374,1.0000388860702516,1.2344506287947297,0.8380141992121936,0.8398237504065037,1.0381346080452205,1.4053251046687365,2.167353528179228,1.9828473469242454,1.528205112926662,1.8880876734852792,2.016520819067955,1.5591710267588497,1.5430319080129267,1.4479076098650694,1.236793963611126,1.3141041703522205,1.5537533987313508,1.5692297449335457,1.121472422592342,1.1581335106864572,0.91726502366364,0.9532682375982404,1.2505696462467313,1.1205617936328052,0.6651569686830044,1.0967526400461791,1.140981236472726,0.6660797173157335,0.8100334141403437,1.2571399945765735,1.1800085892900825,0.9563456442207099,1.2749242424964906,1.1340990519151093,0.9276029605418444,0.5047679111361504,0.9407211143523457,0.6309511506929995,1.074688763730228,1.2769522689282895,0.5026340553537011,0.7528656773269176,1.0695354964584112,0.9779949204996229,1.300148520246148,1.1204699540510774,1.5327852481976152,1.4124552657827738,1.2289950992912055,1.0769147641956807,1.4084996918216348,1.2656738823279738,1.0495817463845016,1.1779037110507489,1.095422700792551,1.3921284958720208,0.6597456347197295,1.0181769583374263,0.9364564327523113,1.3884215405210854,0.9055566122755409,1.1202643141150477,1.596531630679965,1.518569000810385,1.201885962113738,1.5418776268139482,1.3921274995431305,0.8939561096951366,1.1407407995313406,1.4240611214190722,1.4680646168068052,1.164111346192658,1.5423512058332562,0.9587342431768777,1.234714117459953,1.4588959828019143,1.6841880340129138,1.6086150078102948,1.4471713358536364,1.2795427026227117,1.444847053103149,1.002940315194428,1.3102364122867585,0.9022639036178589,1.2806951073929669,0.989768156595528,0.9441032137721775,0.9244450947269796,0.9194099459797145,0.9374097302556038,0.7403792202472688,0.8557088484987617,1.1484702169895173,0.7273479776456953,0.8502402873709798,0.6981262018904091,0.8579837949946523,0.7507739521563054,0.7508660649880767,0.7793322708457708,0.9225482998415828,0.9773600473999976,0.9583356784656645,0.9616499662399293,0.9474486894905567,1.0015693807974457,0.9874830450862646,0.9377102639526129,0.9753739142790437,0.9764441156759859,0.973571441695094,0.950638056918979,0.9416109262034296,0.9724794756621122,0.966675561480224,1.2231912130489944,1.235738294199109,0.9654571769759062 NODERIV
af_dist2: CONSTANT VALUES=0 NODERIV
Rg: GYRATION TYPE=RADIUS ATOMS=1-414
RMSD1: RMSD REFERENCE=struct1.pdb TYPE=OPTIMAL
RMSD2: RMSD REFERENCE=struct2.pdb TYPE=OPTIMAL
RMSD3: RMSD REFERENCE=struct3.pdb TYPE=OPTIMAL
uwall: UPPER_WALLS ARG=RMSD1,RMSD2,RMSD3 AT=0.02,0.02,0.02 KAPPA=100000,100000,100000 EXP=2,2,2 EPS=1,1,1 OFFSET=0,0,0
PRINT FILE=DISTANCE_MAP_REST ARG=distance_rest_domains STRIDE=200
PRINT FILE=COLVAR ARG=__FILL__ STRIDE=200
PBMETAD ...
LABEL=pb
ARG=__FILL__
SIGMA=__FILL__
SIGMA_MIN=__FILL__
SIGMA_MAX=__FILL__
ADAPTIVE=DIFF
HEIGHT=__FILL__
PACE=200
BIASFACTOR=__FILL__
GRID_MIN=__FILL__
GRID_MAX=__FILL__
GRID_WSTRIDE=__FILL__
WALKERS_MPI
TEMP=__FILL__
... PBMETAD
METAINFERENCE ...
ARG=(distance_rest_domains.*),pb.bias REWEIGHT
PARARG=(af_dist_rest
SIGMA_MEAN0=1
NOISETYPE=MGAUSS OPTSIGMAMEAN=SEM AVERAGING=200
SIGMA0=10.0 SIGMA_MIN=0.0001 SIGMA_MAX=10.0 DSIGMA=0.1
MC_STEPS=10
MC_CHUNKSIZE=23
WRITE_STRIDE=10000
TEMP=__FILL__
LABEL=af_mi_rest_domains
... METAINFERENCE
FLUSH STRIDE=200
PRINT FILE=ENERGY ARG=pb.bias STRIDE=200
PRINT ARG=af_mi_rest_domains STRIDE=200 FILE=BAYES_rest_domains
ENDPLUMED