Dear Amber users
I am sumilating one protein in water. Thy system have
8800 water molecules added by solvatebox
command(buffer is 10 angstrom) and have 30000 total
atoms. In order to run the system using amber 6, I
have to change some value in sizes.h file. these
values are changed as follows:
parameter (MAXREA=6500000)
parameter (MAXINT=3000000)
parameter (MAXHOL=600000)
parameter (MAXPR=50000000)
parameter (MAXDUP=15000)
integer
MAX_RSTACK,MAX_ISTACK,MAX_STACK_PTRS,MAX_HEAP_PTRS
parameter (MAX_RSTACK=2500000)
parameter (MAX_ISTACK=150000)
parameter (MAX_STACK_PTRS=200)
parameter (MAX_HEAP_PTRS=200)
MAXPR is set based on the principle: MAXPR >
Natom*(Natom-1)/2=30000*(30000-1)/2.
The first question is :Are these parameters
reasonable?
Then I use " make install" command in sander
directory to reinstall sander. But when I run
minimization, the computation is died. my input file
is below:
$cntrl
imin=1, maxcyc=5000, cut=10.0, ncyc=100, ntmin=1,
ibelly=1, ntpr=100, npscal=1
&end
belly
RES 240 242 283 9041
END
END
And the final output is following:
---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC
SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to
cutoff
| CHECK switch(x): max rel err = 0.3056E-14 at
2.423500
| CHECK d/dx switch(x): max rel err = 0.8711E-11
at 2.747560
---------------------------------------------------
Total number of mask terms = 45519
Total number of mask terms = 91038
| Total Ewald setup time = 0.12000000
------------------------------------------------------
As output above, I find no any error information
presented, so I don't know why the calculation is
died?
Then I try to change cutoff=10.0 to 8.0 in input
file and run once more. But the run still died at the
beggining with error information:
Static Integer Memory requirement of: 2302488
exceeds MAXINT of 2000000
| Memory Use Allocated Used
| Real 2500000 2189632
| Hollerith 600000 188401
| Integer 2000000 2302488
| Max Nonbonded Pairs:15000000
** Redimension and recompile
But I already set MAXINT=3000000 in sizes.h file, why
error information still tell MAXINT=2000000. How I fix
the problem?
Anyone help me? Thanks very much
yb
__________________________________________________
Do you Yahoo!?
Yahoo! Shopping - Send Flowers for Valentine's Day
http://www.rosswalker.co.uk/adsense_alternatives/
Received on Fri Feb 14 2003 - 21:51:13 PST
