Hi,
I am trying to do normal mode analysis on a protein having 6398 atoms. I
energy
minimized the structure using steepest descent followed by L-BFGS minimization
technique
. The Fmax was equal to 9.67927896882578e-07.
I then went on to perform normal mode analysis. The command was
nohup mdrun_d -v -s new_nm.tpr -deffnm new_nm -mtx new_nm.mtx &
Then ,when I tried to diagonalize the matrix , the command being:
g_nmeig_d -f new_nm.mtx -s new_nm.tpr -ol eigenvalue.xvg -v eigenvector.trr
I get the error message as :
g_nmeig_d(1892) malloc: *** mmap(size=18446744072353271808) failed (error
code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
I am using a 8 node computer each with a RAM of 2 GB. ( g_nmeig_d runs on a
single node).
Gromacs has been compiled in 64 bit mode.
I have no clue regarding this problem.
Any suggestion will be of great help.
Thanks in advance.
Sarbani Chattopadhyay
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