Re: [gmx-users] 'SHAKE' : gromacs 4.0.7
When you run GROMACS in parallel, by default it does domain descomposition, so if your constraints run across the charge groups, SHAKE can not run. El mar, 20-04-2010 a las 14:49 -0700, Ramachandran G escribió: > Hello gromacs users: > I installed the new version of gromacs and tried to run > 'mdrun_mpi' in parrallel but it gives the error pasted below. > When i switched the constrain from 'shake' to 'lincs' it runs. I > know 'shake' algorithm compilation was done but i don't why > i am getting this error. The error does not arise when i run it in > serial. Any help will be highly appreciated. > > -- > Program mdrun_mpi_d, VERSION 4.0.7 > Source code file: constr.c, line: 830 > > Fatal error: > SHAKE is not supported with domain decomposition and constraint that > cross charge group boundaries, use LINCS > -- > > best, > Rama > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.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 mailing listgmx-users@gromacs.org http://lists.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] 'SHAKE' : gromacs 4.0.7
Ramachandran G wrote: Hello gromacs users: I installed the new version of gromacs and tried to run 'mdrun_mpi' in parrallel but it gives the error pasted below. When i switched the constrain from 'shake' to 'lincs' it runs. I know 'shake' algorithm compilation was done but i don't why i am getting this error. The error does not arise when i run it in serial. Any help will be highly appreciated. -- Program mdrun_mpi_d, VERSION 4.0.7 Source code file: constr.c, line: 830 Fatal error: SHAKE is not supported with domain decomposition and constraint that cross charge group boundaries, use LINCS -- The error message is really quite explicit. SHAKE + constraints between charge groups = failure. You won't see any error in serial, because you can't run domain decomposition on a single processor. If you want to use SHAKE, either run in serial, or perhaps you can try the old particle decomposition (mdrun -pd), but the results in both cases will certainly be slower than if you use LINCS and domain decomposition. -Justin best, Rama -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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] 'SHAKE' : gromacs 4.0.7
Hello gromacs users: I installed the new version of gromacs and tried to run 'mdrun_mpi' in parrallel but it gives the error pasted below. When i switched the constrain from 'shake' to 'lincs' it runs. I know 'shake' algorithm compilation was done but i don't why i am getting this error. The error does not arise when i run it in serial. Any help will be highly appreciated. -- Program mdrun_mpi_d, VERSION 4.0.7 Source code file: constr.c, line: 830 Fatal error: SHAKE is not supported with domain decomposition and constraint that cross charge group boundaries, use LINCS -- best, Rama -- gmx-users mailing listgmx-users@gromacs.org http://lists.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
