[gmx-users] vacum simulation

[Erik Marklund]

You seem to be using a 2 fs time step. It's difficult to achieve stable integration using 2 fs time steps in vacuum. Please provide more information about your simulation parameters.

Erik

On 2 May 2013, at 14:40, Souilem Safa <safasouilem1 at gmail.com> 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?
> Best regards,
> Safa
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