From: Nara Dashdorj (dnr_at_physics.purdue.edu)
Date: Tue Nov 01 2005 - 22:31:53 CST
Dear NAMD Users:
I have posted the problem titled Serious Steric Clashes, in which NAMD
produced huge VDW energy that lead to thinking of it was caused by
steric clashes. In addition, there were several residues really close to
the heme groups.
However working on this problem with huge help from Brian Bennion (I do
deeply appreciate his help), we narrowed down the problem with IC of the
topology file of the heme groups. The problem was that the minimization
would not know where to go and simply searches for new direction. After
disabling the IC in the topology file, which was developed by Felix
Autenrieth in the following paper, the minimization performed well, and
the problem was solved.
Autenrieth F, Tajkhorshid E, Baudry J, et al.Classical force field parameters for the heme prosthetic group of cytochrome c
JOURNAL OF COMPUTATIONAL CHEMISTRY 25 (13): 1613-1622 OCT 2004
But we did not quite figure out the reason behind it, other than psfgen
was dublicating bonds and angles. So we would love to hear what you have
to say on this regard? On the use of IC in this particular case? We
think that it might be useful for other people using this new topology
and parameter files of heme.
Even though this problem is solved, I do still have another problem. The
simulation is in the packing phase (packing lipid membrane and water
around the protein), so I am doing constant pressure simulation, in
which the protein is constrained (harmonic constraint force constant was
set to 10.00 for the protein). After minimizing for 5000 steps, the
simulation produced the following error and dumped a core:
ENERGY: 5000 21011.7637 33823.0894 28278.1965
435.8856 -579767.5272 106052.3441 7617.8387
0.0000 0.0000 -382548.4092 0.0000
-382548.4092 -382548.4092 0.0000 11070.9745
11099.3686 2333392.6700 11070.9745 11099.3686
REINITIALIZING VELOCITIES AT STEP 5000 TO 310 KELVIN.
TCL: Running for 90000 steps
PRESSURE: 5000 15236.4 20.928 -287.225 -10.7428 15140 -116.998 -108.239
-116.105 15028.9
GPRESSURE: 5000 12744.9 8.26987 -282.398 -17.309 12648.1 -110.176
-98.9749 -101.805 12543.9
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY
MISC KINETIC TOTAL TEMP
TOTAL2 TOTAL3 TEMPAVG PRESSURE
GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 5000 21011.7637 33823.0894 28278.1965
435.8856 -579767.5272 106052.3441 7617.8387
0.0000 202522.1430 -180026.2663 309.7293
-179308.8377 -181999.1948 309.7293 15135.1205
12645.6496 2333392.6700 15135.1205 12645.6496
OPENING EXTENDED SYSTEM TRAJECTORY FILE
ENERGY: 5001 44132.9483 39106.8270 28365.7151
466.9517 -579767.5272 106052.3441 7793.2981
0.0000 184643.4118 -169206.0312 282.3862
-167738.5423 -173429.1407 282.3862 11342.5379
12595.9242 2333392.6700 11342.5379 12595.9242
ENERGY: 5002 60860.9149 46567.5170 28575.7891
532.4782 -576488.2462 107156.9570 8074.9153
0.0000 149195.6849 -175523.9898 228.1739
-173385.4682 -181760.1976 228.1739 13544.2370
12748.2137 2333392.6700 13544.2370 12748.2137
ENERGY: 5003 79254.8581 59333.7262 28914.9292
640.5539 -576488.2462 107156.9570 14606.0549
0.0000 130079.1703 -156501.9966 198.9379
-153996.7101 -163838.4990 198.9379 -29633.7426
-23506.4512 2356056.0442 -29633.7426 -23506.4512
ENERGY: 5004 47597.7888 67703.4792 29276.6569
760.1591 -559694.8595 97201.4692 14843.0688
0.0000 134924.4893 -167387.7483 206.3481
-164787.1383 -174371.2786 206.3481 -25993.2968
-24843.2139 2356056.0442 -25993.2968 -24843.2139
ENERGY: 5005 36524.0367 75559.9082 29650.7446
900.3912 -559694.8595 97201.4692 15080.0365
0.0000 144275.6109 -160502.6622 220.6493
-159374.8375 -163067.8364 220.6493 -25688.0623
-24529.2941 2356056.0442 -25688.0623 -24529.2941
ENERGY: 5006 38328.8817 76176.8261 29950.1793
1024.1189 -543680.6734 109406.3996 15205.3038
0.0000 315729.5499 42140.5859 482.8641
119615.5782 -189466.0912 482.8641 -10187.0936
-14411.8546 2356056.0442 -10187.0936 -14411.8546
ENERGY: 5007 87705.9246 78360.4343 30187.4607
2821.9369 -543680.6734 109406.3996 24578.7959
0.0000 909369.1819 698749.4606 1390.7528
702399.2113 688618.5083 1390.7528 82587.3544
73715.1284 2314969.2215 82587.3544 73715.1284
ERROR: Atom 29957 velocity is 188311 27488.5 -137339 (limit is 10000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 4041 velocity is -248931 -37248 186994 (limit is 10000)
ERROR: Atoms moving too fast; simulation has become unstable.
BUG ALERT: Bad global exclusion count!
BUG ALERT: NAMD has detected a bug. Please notify namd_at_ks.uiuc.edu.
BUG ALERT: Bad global exclusion count!
BUG ALERT: NAMD has detected a bug. Please notify namd_at_ks.uiuc.edu.
Fatal error, aborting.
These two molecules are in the protein, the one 4041 is a carbon
molecule of glycine residue, whereas the other one 29957 is oxygen of
water molecule. The water molecule is proposed to provide ligand to the
iron of the heme group in the crystal structure but since the resolution
is not high enough it is still hypothesis. So in the model, I just left
it there without any bonds to it to test the hypothesis, but during the
minization the iron of the heme and the oxygen of this water came
together, which caused the error, I think! I am not really sure about
what happened to the other one!
So what should one do in this case? Any ideas guys!
Thanks, Nara
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