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AMBER Archive (2005)Subject: AMBER: AMBER8 limitation of memory in QM/MM calculation
From: nadtanet nunthaboot (nadtanet_at_hotmail.com)
Dear Amber users,
I try to use amber 8 with my system up to 50,000 atoms. I would like
I test the program and I found that if the system contains about 3000 atoms,
“ ASSERTion 'ier == 0' failed in sander.f at line 684”
This is error due to limitation of memory. Therefore, I try to increase
I modified sander.f (line before 864), as shown below.
! --- dynamic memory allocation:
! open(101,file='thep')
! write (101,*) lastr,lasti,lastpr
! write (101,*) ipairs(lastpr),lasth
allocate( x(lastr), ix(lasti), ipairs(lastpr), ih(lasth), stat = ier
! allocate( x(lastr), ix(lasti), ipairs(lastpr), ih(lasth) )
REQUIRE( ier == 0 )
After I try to printout of lastr, lasti, lastpr and lasth. I got these
1621806 1081568 1132237491
0 301731
Moreover, I also set limit and now I got
cputime unlimited
filesize unlimited
datasize unlimited
stacksize unlimited
coredumpsize unlimited
memoryuse unlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 32 kbytes
maxproc 16366
I still can not run QM/MM MD because of limitation of memery. Can
Best Regards,
Nadtanet
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