[gmx-users] vacum simulation

[Justin Lemkul]

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

-- 
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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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