Re: help: nmode compile question!!!

From: Andreas Svrcek-Seiler <>
Date: Wed 15 May 2002 13:30:12 +0200 (CEST)

> 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.


           ( O O )
              o Wolfgang Andreas Svrcek-Seiler
              o (godzilla)
      .oooO Tel.:01-4277-52733
      ( ) Oooo.
-------\ (----( )--------------------------------------------------------
        \_) ) /
Received on Wed May 15 2002 - 04:30:12 PDT
Custom Search