Re: No Subject Given By The Author



On Sun, 17 Dec 2000, Sergey Noskov wrote:
 > I have a big problems with memory allocation in CHARMM27b1 bothly on SGI
 > and GNU platfoorms. Unfortunately, I need to make an aproximate normal
 > mode analysis for medium sized protein ( 5362 atom in all hydrogen force
 > field). Options like REDU CMP or DIMB diagonalization does not help in
 > this program. CHARMM error output include a message like :
 >
 > expanded heap on ***** words
 > problem with storage
 > MALLOC set to 0.0
 This indicates that CHARMM asked for some extra memory, which the OS
 could not provide.  Since normal modes require a 3N*3N matrix, the
 memory needed in Mbytes is
 	(8*(3*N)**2)/(1024*1024)	for N=5362	= 1974
 or almost 2 Gbytes of memory.  Your system (IRIX or Linux) needs to have
 a fairly large amount of physical RAM and more that 2 Gbyte of swap
 space configured in order to do this calculation.
 --
 Rick Venable                  =====\     |=|    "Eschew Obfuscation"
 FDA/CBER Biophysics Lab       |____/     |=|
 Bethesda, MD  U.S.A.          |   \    / |=|  ( Not an official statement or
 Rick_Venable;at;nih.gov          |    \  /  |=|    position of the FDA; for
 that,
 rvenable;at;speakeasy.org              \/   |=|    see   http://www.fda.gov  )