[gmx-users] vacum simulation
Souilem Safa
safasouilem1 at gmail.com
Thu May 2 15:11:23 CEST 2013
Thank you very much
On 2 May 2013 22:00, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 5/2/13 8:57 AM, Souilem Safa wrote:
>
>> Thank you for your quick answer
>> I have joined here my mdp file and the toplogy one also.
>>
>
> The mailing list does not accept attachments. Please copy and paste the
> text into an email. We may not need the whole topology, but a description
> of what you're working with is important. If you are using some novel
> molecule for which you've generated parameters, those can be a source of
> problems.
>
>
> Should I increase the time step? I'm sorry I'm new in MD
>>
>>
> Increasing the timestep in the case of instabilities is the exact opposite
> of what you should do. Please read the link I posted earlier.
>
> -Justin
>
>
>
>>
>> On 2 May 2013 21:48, Erik Marklund <erikm at xray.bmc.uu.se> wrote:
>>
>> 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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> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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