AMBER Archive (2005)

Subject: AMBER: memory_mm_pbsa

From: Wei Chen (gtg553p_at_mail.gatech.edu)
Date: Mon Aug 01 2005 - 22:00:34 CDT


Dear Amber users,

I am trying to use mm_pbsa to calculate free energy for protein molecules.
It is a big molecules, having 9536 atoms totally.

So far, I got enthalpy results well. But when I calculated entropy using nmode,
I met memory problem, errors like:

Total memory required : 409700851 real words

Total memory required : 46084583 integer words

Maximum nonbond pairs 45462879
ASSERTion ' ier == 0 ' failed in nmode.f at line 105.

I am wondering whether I can find a way to get around this problem.
Now I am using amber8 in SGI Origin 300 with 8 cpus and 4 GB memory. What kind
of computational system do I need to get this done?

Thanks!

Wei Chen

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