Dear Holger,
thanks for your answers. I am still having problems, though, with
calculating vibrational entropies using nmode via mm_pbsa of 3000-atom
protein.
The problem is with the size of memory arrays (non-bonded pairs). How
can I make them bigger? In compilation (where?) or using more memory?
I'm sending you parts of nmode files, sizes.h and sizes2.h if you please
could have a look and suggest parameters for my case. (I am especially
not sure about nprec=2 and naxdup=800)
If it works, I prefer 64-bit Opterons of 4/8GB memory over Itanium2
Altix3000 which is busy all the time.
Looking forward to hearing from you. Thanks.
Best regards,
Martin Lepsik
----------
nmode.out
Total memory required : 141798148 real words
Total memory avail : 265000000 real words
Total memory required : 213413 integer words
Total memory avail : 4000000 integer words
Maximum nonbond pairs 3786586
Getting coordinates from file with title:
Number of non-bonded pairs = 3812701
Number of H-bonded pairs = 0
Insufficient memory to hold
nonbonded pair list
Memory available for list = 3786586
***** ERROR STOP *****
-------------
sizes.h
c parameter (MAXMEMX=3500000)
parameter (MAXMEMX=190000000)
parameter (MAXMEMI=4000000)
c
c ----- More precisely,
c ----- bit length of an actual real array element
c ----- = nprec * (declared bit length of x)
c ----- provided it is allowed on the machine in use.
c
c ----- nshort should be 1 if all integers use the same
c ----- number of bits and 2 if some short integers use
c ----- half the number of bits needed for a normal integer.
c
c ML:changed to increase array size
parameter (nprec = 2)
c parameter (nprec = 1)
parameter (nshort = 1)
c
c ----- naxdup is the maximum number of dihedrals that can ever
c ----- be duplicated. 400 seems to be a good conserative number,
c ----- unless you have a really big molecule
c
c parameter (naxdup = 400)
c
c ML 2*
parameter (naxdup = 800)
real*8 x (MAXMEMX)
integer ix(MAXMEMI)
common/store_x/ x
common/store_ix/ ix
-------------
sizes2.h
c parameter (MEMDRV=10000000)
c parameter (MAXATOM=2600)
c parameter (MAXINT=200)
c parameter (MAXVEC=500)
c ML dame to 5*vetsi
parameter (MEMDRV=50000000)
parameter (MAXATOM=13000)
parameter (MAXINT=1000)
parameter (MAXVEC=2500)
c
C ----- SET THE LIMITS OF SOME ARRAY BOUNDS -----
C
c parameter (MAXDIH = 5500)
c parameter (MAXDIA = 3500)
c parameter (MAXINB = 9000)
c parameter (MAXBON = 2600)
c parameter (MAXBNH = 2000)
c parameter (MAXANG = 3000)
c parameter (MAXANH = 3000)
c ML dame to 5*vetsi
parameter (MAXDIH = 27500)
parameter (MAXDIA = 17500)
parameter (MAXINB = 45000)
parameter (MAXBON = 13000)
parameter (MAXBNH = 10000)
parameter (MAXANG = 15000)
parameter (MAXANH = 15000)
--------------------------
-----------
Martin Lepsik
Dept. of Molecular Modeling
Institute of Organic Chemistry & Biochemistry
Czech Academy of Sciences
phone: +420-220 183 540
fax:+420-220 183 292
e-mail:lepsik.uochb.cas.cz
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Received on Fri Jan 30 2004 - 18:56:03 PST
