AMBER Archive (2002)

Subject: Re: help: nmode compile question!!!

From: Andreas Svrcek-Seiler (svrci_at_tbi.univie.ac.at)
Date: Wed May 15 2002 - 06:30:12 CDT

Hi,
> I use the AMBER/nmode to do th Normal mode analysis of the protein. this protein is 630 residues. so the src/nmode file size.h was changed. But it still can not work. It say MAXM is too small. when I change the MAXM = 1000000, it crashed after 2 minimute and say "Bus error". I check the nmdout file. It stop at first energy calculation. I do not know way. Can someone help me?
> By the way, I use the AMBER7. Does someone can tell me how to compile the nmode program for large protein?
.... your protein has -say- about 6000 atoms (probably more) - so the
hessian matrix will contain at least (3*6000)**2 >= 3*10**8 double
precision values (maybe only about half of that value, since the HM is
symmetric). So the (mass weighted - that does not matter) hessian alone
will probably require more than 3 (or 1.5) GB of memory.
I haven't looked into the sources of nmode, but I guess unless there
are some truncation/memory saving tricks the problem might come from
the limits of your operating system and/or hardware.

greetings
Andreas

             
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