[gmx-users] Regarding calculation of configurational entropy

[David van der Spoel]

Den 2020-02-04 kl. 07:33, skrev Amit Kumar:
> Dear gromacs user,
> I am trying to calculate configurational entropy using gmx anaeig of
> gromacs, I want to plot entropy vs time graph but I am getting following
> output:
> eigval[5142] = -9.14879e-07
> eigval[5143] = -2.33309e-06
> eigval[5144] = -3.50518e-06
> eigval[5145] = -4.66171e-06
> eigval[5146] = -5.99885e-06
> eigval[5147] = -7.11318e-06
> eigval[5148] = -8.01442e-06
> eigval[5149] = -9.39166e-06
> eigval[5150] = -1.04459e-05
> eigval[5151] = -1.15148e-05
> eigval[5152] = -1.28094e-05
> eigval[5153] = -1.3987e-05
> eigval[5154] = -1.50665e-05
> eigval[5155] = -1.6175e-05
> eigval[5156] = -1.73784e-05
> eigval[5157] = -1.83775e-05
> eigval[5158] = -1.96176e-05
> eigval[5159] = -2.05775e-05
> eigval[5160] = -2.16381e-05
> eigval[5161] = -2.28186e-05
> eigval[5162] = -2.41095e-05
> eigval[5163] = -2.50757e-05
> eigval[5164] = -2.62638e-05
> eigval[5165] = -2.72389e-05
> eigval[5166] = -2.81506e-05
> eigval[5167] = -2.9425e-05
> eigval[5168] = -3.03292e-05
> eigval[5169] = -3.13687e-05
> eigval[5170] = -3.26255e-05
> eigval[5171] = -3.35174e-05
> eigval[5172] = -3.45212e-05
> eigval[5173] = -3.58501e-05
> eigval[5174] = -3.6593e-05
> eigval[5175] = -3.76517e-05
> eigval[5176] = -3.89211e-05
> eigval[5177] = -3.96407e-05
> eigval[5178] = -4.06224e-05
> eigval[5179] = -4.15366e-05
> eigval[5180] = -4.28279e-05
> eigval[5181] = -4.3513e-05
> eigval[5182] = -4.45138e-05
> eigval[5183] = -4.562e-05
> eigval[5184] = -4.65709e-05
> eigval[5185] = -4.76809e-05
> eigval[5186] = -4.86234e-05
> eigval[5187] = -4.92399e-05
> eigval[5188] = -5.05317e-05
> eigval[5189] = -5.15467e-05
> eigval[5190] = -5.22315e-05
> eigval[5191] = -5.34672e-05
> eigval[5192] = -5.43978e-05
> eigval[5193] = -5.51698e-05
> eigval[5194] = -5.61273e-05
> eigval[5195] = -5.69449e-05
> eigval[5196] = -5.79809e-05
> eigval[5197] = -5.89205e-05
> eigval[5198] = -5.97684e-05
> eigval[5199] = -6.03984e-05
> eigval[5200] = -6.12329e-05
> eigval[5201] = -6.2341e-05
> eigval[5202] = -6.314e-05
> eigval[5203] = -6.40677e-05
> eigval[5204] = -6.48297e-05
> eigval[5205] = -6.57083e-05
> eigval[5206] = -6.69065e-05
> eigval[5207] = -6.75107e-05
> eigval[5208] = -6.84447e-05
> eigval[5209] = -6.91988e-05
> eigval[5210] = -6.99852e-05
> eigval[5211] = -7.08491e-05
> eigval[5212] = -7.12099e-05
> eigval[5213] = -7.14211e-05
> eigval[5214] = -7.24288e-05
> eigval[5215] = -7.24905e-05
> eigval[5216] = -7.34137e-05
> eigval[5217] = -7.40195e-05
> eigval[5218] = -7.48026e-05
> eigval[5219] = -7.54402e-05
> eigval[5220] = -7.63235e-05
> eigval[5221] = -7.65044e-05
> eigval[5222] = -7.70526e-05
> eigval[5223] = -7.77833e-05
> eigval[5224] = -7.84475e-05
> eigval[5225] = -7.94353e-05
> eigval[5226] = -8.03098e-05
> eigval[5227] = -8.08805e-05
> eigval[5228] = -8.1798e-05
> eigval[5229] = -8.24363e-05
> eigval[5230] = -8.30689e-05
> eigval[5231] = -8.37781e-05
> eigval[5232] = -8.47785e-05
> eigval[5233] = -8.51702e-05
> eigval[5234] = -8.5924e-05
> eigval[5235] = -8.6987e-05
> eigval[5236] = -8.74341e-05
> eigval[5237] = -8.79993e-05
> eigval[5238] = -8.85487e-05
> eigval[5239] = -8.93534e-05
> eigval[5240] = -9.02589e-05
> eigval[5241] = -9.09801e-05
> eigval[5242] = -9.13512e-05
> eigval[5243] = -9.19218e-05
> eigval[5244] = -9.25432e-05
> eigval[5245] = -9.31305e-05
> eigval[5246] = -9.3984e-05
> eigval[5247] = -9.45856e-05
> eigval[5248] = -9.5029e-05
> eigval[5249] = -9.58923e-05
> eigval[5250] = -9.66012e-05
> eigval[5251] = -9.69965e-05
> eigval[5252] = -9.73971e-05
> eigval[5253] = -9.80373e-05
> eigval[5254] = -9.87206e-05
> eigval[5255] = -9.92092e-05
> eigval[5256] = -9.99034e-05
> eigval[5257] = -0.000100159
> eigval[5258] = -0.000100874
> eigval[5259] = -0.000101257
> eigval[5260] = -0.000101832
> eigval[5261] = -0.000102451
> eigval[5262] = -0.000102838
> eigval[5263] = -0.000103337
> eigval[5264] = -0.000103816
> eigval[5265] = -0.000104062
> eigval[5266] = -0.000104524
> eigval[5267] = -0.00010504
> eigval[5268] = -0.000105673
> eigval[5269] = -0.000105892
> eigval[5270] = -0.000106473
> eigval[5271] = -0.000107099
> eigval[5272] = -0.000107394
> eigval[5273] = -0.000107771
> eigval[5274] = -0.000108434
> eigval[5275] = -0.000108798
> eigval[5276] = -0.000108992
> eigval[5277] = -0.000109278
> eigval[5278] = -0.000109677
> eigval[5279] = -0.000110072
> eigval[5280] = -0.000110326
> eigval[5281] = -0.000110964
> eigval[5282] = -0.000111025
> eigval[5283] = -0.000111309
> eigval[5284] = -0.000112023
> eigval[5285] = -0.000112365
> eigval[5286] = -0.00011257
> eigval[5287] = -0.000112921
> eigval[5288] = -0.000113374
> eigval[5289] = -0.000113933
> eigval[5290] = -0.000114647
> eigval[5291] = -0.000115405
> eigval[5292] = -0.000115669
> eigval[5293] = -0.00011589
> eigval[5294] = -0.000116295
> eigval[5295] = -0.000116993
> eigval[5296] = -0.000117111
> eigval[5297] = -0.000117667
> eigval[5298] = -0.000118582
> eigval[5299] = -0.00011872
> eigval[5300] = -0.000118885
> eigval[5301] = -0.000119334
> eigval[5302] = -0.000120538
> eigval[5303] = -0.00012068
> eigval[5304] = -0.000121256
> eigval[5305] = -0.00012141
> eigval[5306] = -0.000122242
> eigval[5307] = -0.000122789
> eigval[5308] = -0.000123013
> eigval[5309] = -0.000123817
> eigval[5310] = -0.000124575
> eigval[5311] = -0.000124866
> eigval[5312] = -0.000125117
> eigval[5313] = -0.000126223
> eigval[5314] = -0.00012707
> eigval[5315] = -0.000127687
> eigval[5316] = -0.000127919
> eigval[5317] = -0.000128714
> eigval[5318] = -0.000129043
> eigval[5319] = -0.00012939
> eigval[5320] = -0.000129535
> eigval[5321] = -0.000130664
> eigval[5322] = -0.000131691
> eigval[5323] = -0.000132264
> eigval[5324] = -0.000133152
> eigval[5325] = -0.00013381
> eigval[5326] = -0.000134219
> eigval[5327] = -0.000135764
> eigval[5328] = -0.000136149
> eigval[5329] = -0.000138551
> eigval[5330] = -0.000138698
> eigval[5331] = -0.000139432
> eigval[5332] = -0.000139957
> eigval[5333] = -0.000140624
> eigval[5334] = -0.000141187
> eigval[5335] = -0.000141866
> eigval[5336] = -0.000143352
> eigval[5337] = -0.000143514
> eigval[5338] = -0.000145445
> eigval[5339] = -0.000146802
> eigval[5340] = -0.00014872
> eigval[5341] = -0.000149065
> eigval[5342] = -0.000150165
> eigval[5343] = -0.000150618
> eigval[5344] = -0.000152546
> eigval[5345] = -0.000154182
> eigval[5346] = -0.000154271
> eigval[5347] = -0.000156094
> eigval[5348] = -0.00015781
> eigval[5349] = -0.000158271
> eigval[5350] = -0.00015992
> eigval[5351] = -0.000162788
> eigval[5352] = -0.000163307
> eigval[5353] = -0.000166183
> eigval[5354] = -0.000169429
> eigval[5355] = -0.000172062
> eigval[5356] = -0.000173377
> eigval[5357] = -0.000173442
> eigval[5358] = -0.000175975
> eigval[5359] = -0.000179223
> eigval[5360] = -0.000181775
> eigval[5361] = -0.000183321
> eigval[5362] = -0.000185641
> eigval[5363] = -0.000193632
> eigval[5364] = -0.000194667
> eigval[5365] = -0.000232906
> eigval[5366] = -0.000255899
> The Entropy due to the Quasi Harmonic approximation is 27848.4 J/mol K
> The Entropy due to the Schlitter formula is nan J/mol K
> Exact command I used was: gmx anaeig -f nojumpcent1_41.xtc -v
> eig_heav_atom.trr -entropy -temp 298 -s prod1.tpr -n protein-H.ndx -comp
> eig_comp.xvg -rmsf eig_rmsf.xvg -proj eig_proj.xvg -2d 2deig_proj.xvg -b 0
> -e  530000
> before this I had used, gmx covar -f nojumpcent1_41.xtc -s prod1.tpr -o
> eig_heav_atom1.xvg -v eig_heav_atom1.trr -ascii eig_heav_atom1.dat  to get
> covariance matrix (I had also tried calculating mass weighted covariance
> but gmx anaeig didn't run with it). I selected Protein-H for least square
> fit and covariance analysis. Can you help me to understand what is going on
> here and if I made  mistakes then what it is?
> 
> Thank You
> Amit Kumar
> 
Did you use double precision? This is needed to get sufficient accuracy,


-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se