Dear All,
Recently, I'm supprised that sander gives me different output
when it applies different number of CPU on IBM P690(AIX51). The
difference between them initiates at 550steps, and gets larger
at the NPT equlibrium stage, and also production dynamics.
System administrator for this machine told me all the AMBER bugfix
are updated to fix.36.
I'm wondering if this is due to the arrangement of 'SIZE OF NONBOND LIST'
while running sander with different number of CPU?
Here are the output information at the 1st minimization step,
---input for sander minimization---
DNA_drug_complex_WAT 11578atoms 1st_Minimization 1000steps
&cntrl
imin=1, ntx=1, maxcyc=1000, ncyc=200,
ntc=1, ntf=1,
ntb=1, ntp=0,
ntpr=50,
cut=9.0,
ntr=0,
&end
&ewald
&end
--------main difference of output-------
(1cpu):
| Local SIZE OF NONBOND LIST = 2461494
| TOTAL SIZE OF NONBOND LIST = 2461494
(8cpu):
| Local SIZE OF NONBOND LIST = 370628
| TOTAL SIZE OF NONBOND LIST = 2461494
----------------------------------------
(1cpu):
NSTEP ENERGY RMS GMAX NAME NUMBER
550 -4.6614E+04 9.7806E-01 2.2339E+01 O5' 543
BOND = 3037.9037 ANGLE = 176.5293 DIHED = 555.3168
VDWAALS = 7046.6932 EEL = -56278.6230 HBOND = 0.0000
1-4 VDW = 341.6471 1-4 EEL = -1493.6799 RESTRAINT = 0.0000
...........
(8cpu):
NSTEP ENERGY RMS GMAX NAME NUMBER
550 -4.6614E+04 9.7805E-01 2.2339E+01 O5' 543
BOND = 3037.9031 ANGLE = 176.5292 DIHED = 555.3168
VDWAALS = 7046.6917 EEL = -56278.6196 HBOND = 0.0000
1-4 VDW = 341.6471 1-4 EEL = 1493.6799 RESTRAINT = 0.0000
...........
---------------------------------------------------------------------------
sincerely,
sychen.
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Fri Mar 05 2004 - 13:53:00 PST
