Dear Amber users,
I try to use amber 8 with my system up to 50,000 atoms. I would like
to use sander.QMMM. My QM part is about 40 atoms and other are treated as MM
part.
I test the program and I found that if the system contains about 3000 atoms,
it works. However, when I applied to my system (50,000 atoms) I got error
massage like this
“ ASSERTion 'ier == 0' failed in sander.f at line 684”
This is error due to limitation of memory. Therefore, I try to increase
memory in my computer.
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
values.
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
anyone suggest me how I can solve this problem. I'm appreciate for your
suggestion.
Best Regards,
Nadtanet
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Tue Aug 02 2005 - 03:53:01 PDT
