Re: [gmx-users] vacum simulation
many thanks to all of you. I have decreased the time step. Simulation has finished in right conditions On 3 May 2013 03:06, Dr. Vitaly Chaban wrote: > LINCS doesn't like your system... or your system doesn't like LINCS... > > You can decrease the time-step as the simplest action. > > Dr. Vitaly Chaban > > > > > > > > > On Thu, May 2, 2013 at 2:40 PM, Souilem Safa > wrote: > > > Dear Gromacs users , > > I did the simulation of a single molecule in vacum. I have choosed 10 ns > > which corresponds to 500 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 33207281664.00 (between atoms 3 and 6) > > bonds that rotated more than 30 degrees: > > atom 1 atom 2 angle previous, current, constraint length > > 46 47 98.80.1406 3889.8669 0.1000 > > 45 46 79.4 10193.8799 10564.2393 0.1440 > > 43 44 79.60.1033 631.2256 0.1000 > > 42 45 80.1 10193.9062 11014.6123 0.1520 > > 42 43 93.50.1851 4970.4243 0.1440 > > 40 41 76.50.1009 184.9659 0.1000 > > 39 42 90.40.1819 5231.5186 0.1520 > > 39 40 100.00.1502 624.0559 0.1440 > > 37 38 97.10.1001 592.4050 0.1000 > > 36 37 81.40.1469 828.7896 0.1430 > > 35 39 88.60.1742 8071.4395 0.1520 > > 35 36 94.70.1861 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. 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. 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. 68351760. 0.1390 > > 20 21 89.1 8780558. 67941296. 0.1390 > > 20 19 88.5 39924512. 280068256. 0.1530 > > 17 19 92.9 371385600. 509824768. 0.1530 > > 17 18 96.4 394707616. 358144416. 0.1230 > > 17 16 90.0 446916736. 883243840. 0.1360 > > 15 16 98.9 1051905920. 370290400. 0.1430 > > 14 15 100.8 520221760. 522257472. 0.1530 > > 13 14 128.2 1139173888. 3275473920. 0.1390 > > 13 11 155.0 2786396928. 3396753920. 0.1390 > > 11 12 151.7 1220930176. 2911329792. 0.1090 > > 9 11 161.5 369404096. 342864. 0.1390 > > 9 10 135.8 2190610944. 1502276608. 0.1090 > > 7 8 91.7 148944928. 1389486464. 0.1000 > > 6 9 150.6 497182528. 4613532672. 0.1390 > > 6 7 168.3 1652069120. 3562507776. 0.1360 > > 4 5 165.5 55138408. 449667456. 0.1000 > > 3 6 169.0 1702803200. 4615812096. 0.1390 > > 3 4 124.7 198457328. 2500093184. 0.1360 > > 13 1 158.1 1042088320. 3730094848. 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 listgmx-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 > > > -- > gmx-users mailing listgmx-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 > -- gmx-users mailing listgmx-users@gromacs.org http://lists
Re: [gmx-users] vacum simulation
LINCS doesn't like your system... or your system doesn't like LINCS... You can decrease the time-step as the simplest action. Dr. Vitaly Chaban On Thu, May 2, 2013 at 2:40 PM, Souilem Safa wrote: > Dear Gromacs users , > I did the simulation of a single molecule in vacum. I have choosed 10 ns > which corresponds to 500 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 33207281664.00 (between atoms 3 and 6) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 46 47 98.80.1406 3889.8669 0.1000 > 45 46 79.4 10193.8799 10564.2393 0.1440 > 43 44 79.60.1033 631.2256 0.1000 > 42 45 80.1 10193.9062 11014.6123 0.1520 > 42 43 93.50.1851 4970.4243 0.1440 > 40 41 76.50.1009 184.9659 0.1000 > 39 42 90.40.1819 5231.5186 0.1520 > 39 40 100.00.1502 624.0559 0.1440 > 37 38 97.10.1001 592.4050 0.1000 > 36 37 81.40.1469 828.7896 0.1430 > 35 39 88.60.1742 8071.4395 0.1520 > 35 36 94.70.1861 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. 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. 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. 68351760. 0.1390 > 20 21 89.1 8780558. 67941296. 0.1390 > 20 19 88.5 39924512. 280068256. 0.1530 > 17 19 92.9 371385600. 509824768. 0.1530 > 17 18 96.4 394707616. 358144416. 0.1230 > 17 16 90.0 446916736. 883243840. 0.1360 > 15 16 98.9 1051905920. 370290400. 0.1430 > 14 15 100.8 520221760. 522257472. 0.1530 > 13 14 128.2 1139173888. 3275473920. 0.1390 > 13 11 155.0 2786396928. 3396753920. 0.1390 > 11 12 151.7 1220930176. 2911329792. 0.1090 > 9 11 161.5 369404096. 342864. 0.1390 > 9 10 135.8 2190610944. 1502276608. 0.1090 > 7 8 91.7 148944928. 1389486464. 0.1000 > 6 9 150.6 497182528. 4613532672. 0.1390 > 6 7 168.3 1652069120. 3562507776. 0.1360 > 4 5 165.5 55138408. 449667456. 0.1000 > 3 6 169.0 1702803200. 4615812096. 0.1390 > 3 4 124.7 198457328. 2500093184. 0.1360 > 13 1 158.1 1042088320. 3730094848. 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 listgmx-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 > -- gmx-users mailing listgmx-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
Re: [gmx-users] vacum simulation
Thank you very much On 2 May 2013 22:00, Justin Lemkul 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 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 wrote: >>> >>> Dear Gromacs users , I did the simulation of a single molecule in vacum. I have choosed 10 ns which corresponds to 500 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 33207281664.00 (between atoms 3 and 6) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 46 47 98.80.1406 3889.8669 0.1000 45 46 79.4 10193.8799 10564.2393 0.1440 43 44 79.60.1033 631.2256 0.1000 42 45 80.1 10193.9062 11014.6123 0.1520 42 43 93.50.1851 4970.4243 0.1440 40 41 76.50.1009 184.9659 0.1000 39 42 90.40.1819 5231.5186 0.1520 39 40 100.00.1502 624.0559 0.1440 37 38 97.10.1001 592.4050 0.1000 36 37 81.40.1469 828.7896 0.1430 35 39 88.60.1742 8071.4395 0.1520 35 36 94.70.1861 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. 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. 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. 68351760. 0.1390 20 21 89.1 8780558. 67941296. 0.1390 20 19 88.5 39924512. 280068256. 0.1530 17 19 92.9 371385600. 509824768. 0.1530 17 18 96.4 394707616. 358144416. 0.1230 17 16 90.0 446916736. 883243840. 0.1360 15 16 98.9 1051905920. 370290400. 0.1430 14 15 100.8 520221760. 522257472. 0.1530 13 14 128.2 1139173888. 3275473920. 0.1390 13 11 155.0 2786396928. 3396753920. 0.1390 11 12 151.7 1220930176. 2911329792. 0.1090 9 11 161.5 369404096. 342864. 0.1390 9 10 135.8 2190610944. 1502276608. 0.1090 7 8 91.7 148944928. 1389486464. 0.1000 6 9 150.6 497182528. 4613532672. 0.1390 6 7 168.3 1652069120. 3562507776. 0.1360 4 5 165.5 55138408. 449667456. 0.1000 3 6 169.0 1702803200. 4615812096. 0.1390 3 4 124.7 198457328. 2500093184. 0.1360 13 1 158.1 1042088320. 3730094848. 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 listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users
Re: [gmx-users] vacum simulation
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 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 wrote: Dear Gromacs users , I did the simulation of a single molecule in vacum. I have choosed 10 ns which corresponds to 500 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 33207281664.00 (between atoms 3 and 6) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 46 47 98.80.1406 3889.8669 0.1000 45 46 79.4 10193.8799 10564.2393 0.1440 43 44 79.60.1033 631.2256 0.1000 42 45 80.1 10193.9062 11014.6123 0.1520 42 43 93.50.1851 4970.4243 0.1440 40 41 76.50.1009 184.9659 0.1000 39 42 90.40.1819 5231.5186 0.1520 39 40 100.00.1502 624.0559 0.1440 37 38 97.10.1001 592.4050 0.1000 36 37 81.40.1469 828.7896 0.1430 35 39 88.60.1742 8071.4395 0.1520 35 36 94.70.1861 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. 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. 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. 68351760. 0.1390 20 21 89.1 8780558. 67941296. 0.1390 20 19 88.5 39924512. 280068256. 0.1530 17 19 92.9 371385600. 509824768. 0.1530 17 18 96.4 394707616. 358144416. 0.1230 17 16 90.0 446916736. 883243840. 0.1360 15 16 98.9 1051905920. 370290400. 0.1430 14 15 100.8 520221760. 522257472. 0.1530 13 14 128.2 1139173888. 3275473920. 0.1390 13 11 155.0 2786396928. 3396753920. 0.1390 11 12 151.7 1220930176. 2911329792. 0.1090 9 11 161.5 369404096. 342864. 0.1390 9 10 135.8 2190610944. 1502276608. 0.1090 7 8 91.7 148944928. 1389486464. 0.1000 6 9 150.6 497182528. 4613532672. 0.1390 6 7 168.3 1652069120. 3562507776. 0.1360 4 5 165.5 55138408. 449667456. 0.1000 3 6 169.0 1702803200. 4615812096. 0.1390 3 4 124.7 198457328. 2500093184. 0.1360 13 1 158.1 1042088320. 3730094848. 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 listgmx-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 -- gmx-users mailing listgmx-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 p
Re: [gmx-users] vacum simulation
Thank you for your quick answer I have joined here my mdp file and the toplogy one also. Should I increase the time step? I'm sorry I'm new in MD On 2 May 2013 21:48, Erik Marklund 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 wrote: > > > Dear Gromacs users , > > I did the simulation of a single molecule in vacum. I have choosed 10 ns > > which corresponds to 500 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 33207281664.00 (between atoms 3 and 6) > > bonds that rotated more than 30 degrees: > > atom 1 atom 2 angle previous, current, constraint length > > 46 47 98.80.1406 3889.8669 0.1000 > > 45 46 79.4 10193.8799 10564.2393 0.1440 > > 43 44 79.60.1033 631.2256 0.1000 > > 42 45 80.1 10193.9062 11014.6123 0.1520 > > 42 43 93.50.1851 4970.4243 0.1440 > > 40 41 76.50.1009 184.9659 0.1000 > > 39 42 90.40.1819 5231.5186 0.1520 > > 39 40 100.00.1502 624.0559 0.1440 > > 37 38 97.10.1001 592.4050 0.1000 > > 36 37 81.40.1469 828.7896 0.1430 > > 35 39 88.60.1742 8071.4395 0.1520 > > 35 36 94.70.1861 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. 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. 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. 68351760. 0.1390 > > 20 21 89.1 8780558. 67941296. 0.1390 > > 20 19 88.5 39924512. 280068256. 0.1530 > > 17 19 92.9 371385600. 509824768. 0.1530 > > 17 18 96.4 394707616. 358144416. 0.1230 > > 17 16 90.0 446916736. 883243840. 0.1360 > > 15 16 98.9 1051905920. 370290400. 0.1430 > > 14 15 100.8 520221760. 522257472. 0.1530 > > 13 14 128.2 1139173888. 3275473920. 0.1390 > > 13 11 155.0 2786396928. 3396753920. 0.1390 > > 11 12 151.7 1220930176. 2911329792. 0.1090 > > 9 11 161.5 369404096. 342864. 0.1390 > > 9 10 135.8 2190610944. 1502276608. 0.1090 > > 7 8 91.7 148944928. 1389486464. 0.1000 > > 6 9 150.6 497182528. 4613532672. 0.1390 > > 6 7 168.3 1652069120. 3562507776. 0.1360 > > 4 5 165.5 55138408. 449667456. 0.1000 > > 3 6 169.0 1702803200. 4615812096. 0.1390 > > 3 4 124.7 198457328. 2500093184. 0.1360 > > 13 1 158.1 1042088320. 3730094848. 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 listgmx-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 > > -- > gmx-users mailing listgmx-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 > -- gmx-users mailing listgmx-users@gromacs.org htt
Re: [gmx-users] vacum simulation
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 wrote: > Dear Gromacs users , > I did the simulation of a single molecule in vacum. I have choosed 10 ns > which corresponds to 500 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 33207281664.00 (between atoms 3 and 6) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 46 47 98.80.1406 3889.8669 0.1000 > 45 46 79.4 10193.8799 10564.2393 0.1440 > 43 44 79.60.1033 631.2256 0.1000 > 42 45 80.1 10193.9062 11014.6123 0.1520 > 42 43 93.50.1851 4970.4243 0.1440 > 40 41 76.50.1009 184.9659 0.1000 > 39 42 90.40.1819 5231.5186 0.1520 > 39 40 100.00.1502 624.0559 0.1440 > 37 38 97.10.1001 592.4050 0.1000 > 36 37 81.40.1469 828.7896 0.1430 > 35 39 88.60.1742 8071.4395 0.1520 > 35 36 94.70.1861 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. 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. 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. 68351760. 0.1390 > 20 21 89.1 8780558. 67941296. 0.1390 > 20 19 88.5 39924512. 280068256. 0.1530 > 17 19 92.9 371385600. 509824768. 0.1530 > 17 18 96.4 394707616. 358144416. 0.1230 > 17 16 90.0 446916736. 883243840. 0.1360 > 15 16 98.9 1051905920. 370290400. 0.1430 > 14 15 100.8 520221760. 522257472. 0.1530 > 13 14 128.2 1139173888. 3275473920. 0.1390 > 13 11 155.0 2786396928. 3396753920. 0.1390 > 11 12 151.7 1220930176. 2911329792. 0.1090 > 9 11 161.5 369404096. 342864. 0.1390 > 9 10 135.8 2190610944. 1502276608. 0.1090 > 7 8 91.7 148944928. 1389486464. 0.1000 > 6 9 150.6 497182528. 4613532672. 0.1390 > 6 7 168.3 1652069120. 3562507776. 0.1360 > 4 5 165.5 55138408. 449667456. 0.1000 > 3 6 169.0 1702803200. 4615812096. 0.1390 > 3 4 124.7 198457328. 2500093184. 0.1360 > 13 1 158.1 1042088320. 3730094848. 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 listgmx-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 -- gmx-users mailing listgmx-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
Re: [gmx-users] vacum simulation
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 500 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 33207281664.00 (between atoms 3 and 6) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 46 47 98.80.1406 3889.8669 0.1000 45 46 79.4 10193.8799 10564.2393 0.1440 43 44 79.60.1033 631.2256 0.1000 42 45 80.1 10193.9062 11014.6123 0.1520 42 43 93.50.1851 4970.4243 0.1440 40 41 76.50.1009 184.9659 0.1000 39 42 90.40.1819 5231.5186 0.1520 39 40 100.00.1502 624.0559 0.1440 37 38 97.10.1001 592.4050 0.1000 36 37 81.40.1469 828.7896 0.1430 35 39 88.60.1742 8071.4395 0.1520 35 36 94.70.1861 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. 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. 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. 68351760. 0.1390 20 21 89.1 8780558. 67941296. 0.1390 20 19 88.5 39924512. 280068256. 0.1530 17 19 92.9 371385600. 509824768. 0.1530 17 18 96.4 394707616. 358144416. 0.1230 17 16 90.0 446916736. 883243840. 0.1360 15 16 98.9 1051905920. 370290400. 0.1430 14 15 100.8 520221760. 522257472. 0.1530 13 14 128.2 1139173888. 3275473920. 0.1390 13 11 155.0 2786396928. 3396753920. 0.1390 11 12 151.7 1220930176. 2911329792. 0.1090 9 11 161.5 369404096. 342864. 0.1390 9 10 135.8 2190610944. 1502276608. 0.1090 7 8 91.7 148944928. 1389486464. 0.1000 6 9 150.6 497182528. 4613532672. 0.1390 6 7 168.3 1652069120. 3562507776. 0.1360 4 5 165.5 55138408. 449667456. 0.1000 3 6 169.0 1702803200. 4615812096. 0.1390 3 4 124.7 198457328. 2500093184. 0.1360 13 1 158.1 1042088320. 3730094848. 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 -- 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 -- gmx-users mailing listgmx-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
[gmx-users] vacum simulation
Dear Gromacs users , I did the simulation of a single molecule in vacum. I have choosed 10 ns which corresponds to 500 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 33207281664.00 (between atoms 3 and 6) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 46 47 98.80.1406 3889.8669 0.1000 45 46 79.4 10193.8799 10564.2393 0.1440 43 44 79.60.1033 631.2256 0.1000 42 45 80.1 10193.9062 11014.6123 0.1520 42 43 93.50.1851 4970.4243 0.1440 40 41 76.50.1009 184.9659 0.1000 39 42 90.40.1819 5231.5186 0.1520 39 40 100.00.1502 624.0559 0.1440 37 38 97.10.1001 592.4050 0.1000 36 37 81.40.1469 828.7896 0.1430 35 39 88.60.1742 8071.4395 0.1520 35 36 94.70.1861 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. 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. 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. 68351760. 0.1390 20 21 89.1 8780558. 67941296. 0.1390 20 19 88.5 39924512. 280068256. 0.1530 17 19 92.9 371385600. 509824768. 0.1530 17 18 96.4 394707616. 358144416. 0.1230 17 16 90.0 446916736. 883243840. 0.1360 15 16 98.9 1051905920. 370290400. 0.1430 14 15 100.8 520221760. 522257472. 0.1530 13 14 128.2 1139173888. 3275473920. 0.1390 13 11 155.0 2786396928. 3396753920. 0.1390 11 12 151.7 1220930176. 2911329792. 0.1090 9 11 161.5 369404096. 342864. 0.1390 9 10 135.8 2190610944. 1502276608. 0.1090 7 8 91.7 148944928. 1389486464. 0.1000 6 9 150.6 497182528. 4613532672. 0.1390 6 7 168.3 1652069120. 3562507776. 0.1360 4 5 165.5 55138408. 449667456. 0.1000 3 6 169.0 1702803200. 4615812096. 0.1390 3 4 124.7 198457328. 2500093184. 0.1360 13 1 158.1 1042088320. 3730094848. 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 listgmx-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
