AMBER Archive (2002)

Subject: nmode memory requirements

From: Michael Jakusch (mjakusch_at_pharma.anbi.ethz.ch)
Date: Fri Jan 18 2002 - 10:15:52 CST


Dear AMBER users/developers,

I just try to run nmode for the first time. With a protein of ~5000
atoms I got one of the familiar memory shortage messages:

Total memory required : 235879241 real words
Total memory avail : 3500000 real words

So I tried to increase the value of MAXMEMX (in sizes.h), because this
was set to 3500000 before. This resulted in the compiler to complain
about:

_nmode_.f:54:
         real*8 x (MAXMEMX)
                ^
Array `x' at (^) is too large to handle

This seems to be a problem of the compiler (g77), in the first
place. However, even if a different compiler could do the job, this
would still be much more than the physical ram of my machine (Athlon
with 256M).

Is normal mode analysis really so demanding that it can hardly be done
on usual proteins???

Regards

        Michael

-- 
Dr. Michael Jakusch

ETH - Swiss Federal Institute of Technology Department of Applied Biosciences Winterthurerstrasse 190 CH-8057 Zürich Switzerland Phone: +41.1.635 60 71 Fax: +41.1.635 68 84 email: michael.jakusch_at_pharma.anbi.ethz.ch