Re: [gmx-users] Range checking error: only on double precision
I guess its the amber03 force field I'm having issues with. The lysozyme tutorial works if I use -ff G43a2 Thanks Jack On Tue, Mar 17, 2009 at 8:01 PM, Justin A. Lemkul wrote: > > Well, several tutorials use lysozyme, PDB 1AKI. I would also recommend not > using ffamber if you are running automated tests, since there are quirks > with requiring specific nomenclature (for lysine, histidine, terminal > residues, etc). > > -Justin > > Jack Shultz wrote: >> >> Justin, >> >> Can you suggest any pdb files I could use that are more simple? I've >> been trying to use files from tutorials but it seems like are always >> problematic. >> >> Jack >> >> On Tue, Mar 17, 2009 at 7:20 PM, Justin A. Lemkul wrote: >>> >>> Jack Shultz wrote: Hello, I just wanted to compare results between single and double precision. I reused the same parameters. Single works. Double caused errors on mdrun. Any idea why? http://hydrogenathome.org/result.php?resultid=1292662 >>> I don't know why any of that worked at all. You've got missing atoms and >>> inconsistent naming (LYSH should be LYP if you really want a protonated >>> lysine under the Amber ports, etc). Did you give pdb2gmx -missing? >>> Otherwise, topology generation should have failed. >>> >>> Especially troublesome: >>> >>> System has non-zero total charge: -2.309866e+01 >>> >>> I would suggest running tests on a physically realistic system that has >>> all >>> atoms present and an integer charge. Maybe single precision somehow >>> overcame these topology problems, but I wouldn't trust any of the >>> results. >>> >>> -Justin >>> --- Program mdrun, VERSION 4.0.3 Source code file: nsgrid.c, line: 357 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 300 ] >>> -- >>> >>> >>> Justin A. Lemkul >>> Graduate Research Assistant >>> ICTAS Doctoral Scholar >>> 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 list gmx-us...@gromacs.org >>> http://www.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >>> >> >> >> > > -- > > > Justin A. Lemkul > Graduate Research Assistant > ICTAS Doctoral Scholar > 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 list gmx-us...@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Range checking error: only on double precision
Well, several tutorials use lysozyme, PDB 1AKI. I would also recommend not using ffamber if you are running automated tests, since there are quirks with requiring specific nomenclature (for lysine, histidine, terminal residues, etc). -Justin Jack Shultz wrote: Justin, Can you suggest any pdb files I could use that are more simple? I've been trying to use files from tutorials but it seems like are always problematic. Jack On Tue, Mar 17, 2009 at 7:20 PM, Justin A. Lemkul wrote: Jack Shultz wrote: Hello, I just wanted to compare results between single and double precision. I reused the same parameters. Single works. Double caused errors on mdrun. Any idea why? http://hydrogenathome.org/result.php?resultid=1292662 I don't know why any of that worked at all. You've got missing atoms and inconsistent naming (LYSH should be LYP if you really want a protonated lysine under the Amber ports, etc). Did you give pdb2gmx -missing? Otherwise, topology generation should have failed. Especially troublesome: System has non-zero total charge: -2.309866e+01 I would suggest running tests on a physically realistic system that has all atoms present and an integer charge. Maybe single precision somehow overcame these topology problems, but I wouldn't trust any of the results. -Justin --- Program mdrun, VERSION 4.0.3 Source code file: nsgrid.c, line: 357 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 300 ] -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Range checking error: only on double precision
Justin, Can you suggest any pdb files I could use that are more simple? I've been trying to use files from tutorials but it seems like are always problematic. Jack On Tue, Mar 17, 2009 at 7:20 PM, Justin A. Lemkul wrote: > > > Jack Shultz wrote: >> >> Hello, >> >> I just wanted to compare results between single and double precision. >> I reused the same parameters. Single works. Double caused errors on >> mdrun. Any idea why? >> >> http://hydrogenathome.org/result.php?resultid=1292662 >> > > I don't know why any of that worked at all. You've got missing atoms and > inconsistent naming (LYSH should be LYP if you really want a protonated > lysine under the Amber ports, etc). Did you give pdb2gmx -missing? > Otherwise, topology generation should have failed. > > Especially troublesome: > > System has non-zero total charge: -2.309866e+01 > > I would suggest running tests on a physically realistic system that has all > atoms present and an integer charge. Maybe single precision somehow > overcame these topology problems, but I wouldn't trust any of the results. > > -Justin > >> --- >> Program mdrun, VERSION 4.0.3 >> Source code file: nsgrid.c, line: 357 >> >> Range checking error: >> Explanation: During neighborsearching, we assign each particle to a grid >> based on its coordinates. If your system contains collisions or parameter >> errors that give particles very high velocities you might end up with some >> coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot >> put these on a grid, so this is usually where we detect those errors. >> Make sure your system is properly energy-minimized and that the potential >> energy seems reasonable before trying again. >> >> Variable ci has value -2147483648. It should have been within [ 0 .. 300 ] >> >> >> > > -- > > > Justin A. Lemkul > Graduate Research Assistant > ICTAS Doctoral Scholar > 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 list gmx-us...@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Range checking error: only on double precision
Jack Shultz wrote: Hello, I just wanted to compare results between single and double precision. I reused the same parameters. Single works. Double caused errors on mdrun. Any idea why? http://hydrogenathome.org/result.php?resultid=1292662 I don't know why any of that worked at all. You've got missing atoms and inconsistent naming (LYSH should be LYP if you really want a protonated lysine under the Amber ports, etc). Did you give pdb2gmx -missing? Otherwise, topology generation should have failed. Especially troublesome: System has non-zero total charge: -2.309866e+01 I would suggest running tests on a physically realistic system that has all atoms present and an integer charge. Maybe single precision somehow overcame these topology problems, but I wouldn't trust any of the results. -Justin --- Program mdrun, VERSION 4.0.3 Source code file: nsgrid.c, line: 357 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 300 ] -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Range checking error: only on double precision
Hello, I just wanted to compare results between single and double precision. I reused the same parameters. Single works. Double caused errors on mdrun. Any idea why? http://hydrogenathome.org/result.php?resultid=1292662 --- Program mdrun, VERSION 4.0.3 Source code file: nsgrid.c, line: 357 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 300 ] -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
