On 5/2/13 8:40 AM, Souilem Safa wrote:
Dear Gromacs users ,
I did the simulation of a single molecule in vacum. I have choosed 10 ns
which corresponds to 5000000 steps. I was checking the .log file frequently.
I have noticed that the number of steps from 1938900 didn't increases.
When I open a new tab with the top option, I see mdrun still existing.
I have attached here the .log file and also some warnings that I saw when
steps stop at 1938900
Step 1938969, time 3877.94 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 12871303501.643789, max 33207281664.000000 (between atoms 3 and 6)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
46 47 98.8 0.1406 3889.8669 0.1000
45 46 79.4 10193.8799 10564.2393 0.1440
43 44 79.6 0.1033 631.2256 0.1000
42 45 80.1 10193.9062 11014.6123 0.1520
42 43 93.5 0.1851 4970.4243 0.1440
40 41 76.5 0.1009 184.9659 0.1000
39 42 90.4 0.1819 5231.5186 0.1520
39 40 100.0 0.1502 624.0559 0.1440
37 38 97.1 0.1001 592.4050 0.1000
36 37 81.4 0.1469 828.7896 0.1430
35 39 88.6 0.1742 8071.4395 0.1520
35 36 94.7 0.1861 8093.3452 0.1530
35 34 92.9 8046.3804 17904.5762 0.1440
33 45 78.0 26093.2402 332765.5000 0.1520
33 34 94.6 26065.5371 330302.5625 0.1440
29 30 74.4 190965.5938 1213272.0000 0.1360
27 28 91.2 85465.0547 294693.5000 0.1430
25 27 85.7 126649.9141 1143663.7500 0.1360
25 26 107.7 116051.3750 805165.8125 0.1230
24 29 102.8 1939418.3750 1702562.5000 0.1390
24 25 101.0 1963544.3750 1402288.3750 0.1390
22 23 97.9 345568.0625 1364901.0000 0.1530
31 21 109.7 1948370.1250 7003795.5000 0.1390
21 22 101.2 2108572.2500 6662917.5000 0.1390
20 24 89.4 8876732.0000 68351760.0000 0.1390
20 21 89.1 8780558.0000 67941296.0000 0.1390
20 19 88.5 39924512.0000 280068256.0000 0.1530
17 19 92.9 371385600.0000 509824768.0000 0.1530
17 18 96.4 394707616.0000 358144416.0000 0.1230
17 16 90.0 446916736.0000 883243840.0000 0.1360
15 16 98.9 1051905920.0000 370290400.0000 0.1430
14 15 100.8 520221760.0000 522257472.0000 0.1530
13 14 128.2 1139173888.0000 3275473920.0000 0.1390
13 11 155.0 2786396928.0000 3396753920.0000 0.1390
11 12 151.7 1220930176.0000 2911329792.0000 0.1090
9 11 161.5 369404096.0000 3428640000.0000 0.1390
9 10 135.8 2190610944.0000 1502276608.0000 0.1090
7 8 91.7 148944928.0000 1389486464.0000 0.1000
6 9 150.6 497182528.0000 4613532672.0000 0.1390
6 7 168.3 1652069120.0000 3562507776.0000 0.1360
4 5 165.5 55138408.0000 449667456.0000 0.1000
3 6 169.0 1702803200.0000 4615812096.0000 0.1390
3 4 124.7 198457328.0000 2500093184.0000 0.1360
13 1 158.1 1042088320.0000 3730094848.0000 0.1390
Wrote pdb files with previous and current coordinates
Please I need your help what should I do in this case?
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
Probably something is wrong in your topology or .mdp file, but since you've
provided neither, it's hard to provide any specific advice.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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