Respected researchers:
First i performed 10 ns simulation using gromacs and after that i calculated binding energy of complex using g_mmpbsa successfully and at this time my GPU was not ON.
Then i deleted my gromacs and reinstalled it to get GPU ON and i got success after that i performed 50 ns simulation using gromacs(this time through GPU) and now i am calculating binding energy of my complex and it give error.
Program g_mmpbsa, VERSION 5.1.2
Source code file: /home/rajendra/software/gromacs_source/gromacs-5.1.2/src/gromacs/utility/smalloc.c, line: 182
Fatal error:
Not enough memory. Failed to calloc 455977412 elements of size 4 for cmap_grid->cmapdata[i].cmap
(called from file /home/rajendra/software/gromacs_source/gromacs-5.1.2/src/gromacs/fileio/tpxio.c, line 2786)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
: Cannot allocate memory
Check this link. This might be helpful for you.
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-January/103078.html
You have problem in mmpbsa installation or try reduce the trajectory frames.
Nikhil Maroli i have also reinstall g_mmpbsa and also reduce may trj frames from 200 to 50 but it doesn't work.
did you installed APBS? the problem will be solved if you installed the correct versions. You can observe in the system information about the memory usage, if its not rising- the problem is with installation.
Nikhil Maroli no, i didn,t install APBS. I simply install g_mmpbsa and also calculated my complex(10ns) binding energy successfully but when i reinstalled my gromacs to ON GPU and did 50 ns simulation and now i am calculating complex binding it give that error,
Program g_mmpbsa, VERSION 5.1.2
Source code file: /home/rajendra/software/gromacs_source/gromacs-5.1.2/src/gromacs/utility/smalloc.c, line: 182
Fatal error:
Not enough memory. Failed to calloc 455977412 elements of size 4 for cmap_grid->cmapdata[i].cmap
(called from file /home/rajendra/software/gromacs_source/gromacs-5.1.2/src/gromacs/fileio/tpxio.c, line 2786)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
: Cannot allocate memory
Hi Said Hassan Khan . Check this out: https://gromacs.org-gmx-users.maillist.sys.kth.narkive.com/s7Prjdo0/not-enough-memory-failed-to-calloc
I think you may be facing a version incompatibility. Did you re-installed the same Gromacs version?
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