[gmx-users] vacum simulation
Justin Lemkul
jalemkul at vt.edu
Thu May 2 15:00:44 CEST 2013
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
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