Thank you very much
On 2 May 2013 22:00, Justin Lemkul <jalem...@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 <er...@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 <safasouil...@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 >>>> -- >>>> gmx-users mailing list gmx-users@gromacs.org >>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>>> * Please search the archive at >>>> >>> http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before >>> posting! >>> >>>> * Please don't post (un)subscribe requests to the list. Use the >>>> www interface or send it to gmx-users-requ...@gromacs.org. >>>> * Can't post? Read >>>> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>>> >>> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> * Please search the archive at >>> http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before >>> posting! >>> * Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to gmx-users-requ...@gromacs.org. >>> * Can't post? Read >>> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> >>> >>> >>> > -- > ==============================**========== > > 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> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
