[gmx-users] Regarding calculation of configurational entropy

[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