AMBER Archive (2005)

Subject: AMBER: AMBER8 limitation of memory in QM/MM calculation

From: nadtanet nunthaboot (nadtanet_at_hotmail.com)
Date: Mon Aug 01 2005 - 21:21:59 CDT


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_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu