Dear all,
I'm trying to do MD simulations using AMBER18 for large systems in explicit
solvent. Amber seems able to be able to handle a size of 1.09 million atoms
very well.However, trying to minimize a system with over 2 million atoms did
not work, giving the error message given below. The minimization tried using
sander.MPI with -np 32. The computer running the simulations has 128 GB RAM and
4x 1080Ti GPU.
Before giving up trying the simulations in explicit solvent, I'd like to know
if a large system like this can be handled in AMBER? what is the size limit to
try?
Any advice on simulating large systems will be appreciated!
Thanks,Ibrahim
>>>>>>>>>>>>>>>>>>>>>>>>>>* NB pairs 264 0 exceeds capacity
( -6648296) 21 SIZE OF NONBOND LIST = -6648296 SANDER BOMB in
subroutine nonbond_list Non bond list overflow! check MAXPR in
locmem.F90--------------------------------------------------------------------------MPI_ABORT was invoked on rank 21 in communicator MPI_COMM_WORLDwith errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.You may or may not see output from other processes, depending onexactly when Open MPI kills them.--------------------------------------------------------------------------
* NB pairs 357 0 exceeds capacity ( -6648296) 8 SIZE OF NONBOND LIST = -6648296 SANDER BOMB in subroutine nonbond_list Non bond list overflow! check MAXPR in locmem.F90
* NB pairs 275 0 exceeds capacity ( -6648296) 13 SIZE OF NONBOND LIST = -6648296 SANDER BOMB in subroutine nonbond_list Non bond list overflow!check MAXPR in locmem.F90
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
Ibrahim M.Moustafa, Ph.D.
Pennsylvania State University
Biochemistry & Molecular Biology Dept.
Millennium Science Complex
University Park, PA16802
Tel (814)863 5940
Fax (814)865 7927
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Received on Mon Dec 10 2018 - 09:30:02 PST
