Dear all
I perfomed replica exchage MD with Amber8 and Amber9 , Both systems are
quite same.
The calculation successed when I used Amber8 but not when I used Amber9. I
think this is very strange.
Then when I used Amber9 , I've got the following error message.
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 1 153 315 317
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
Why did I get the error message and stop calculation only when I used
Amber9?
This is my sander script with Amber9.
sander.MPI -ng 16 -rem 1 -remlog rem.log -groupfile groupfile"
And my groupfile is
-O -i REM.in.000 -p INIT.top -o REM.out.000 -c md.rst.000 -r REM.rst.000 -x
REM.trj.000
-O -i REM.in.001 -p INIT.top -o REM.out.001 -c md.rst.001 -r REM.rst.001 -x
REM.trj.001
I set REM.in.000 file the following.
&cntrl
ntx=5, irest=1,
ntf=2, ntc=2,
ntt=1,
ntb=0, igb=2, saltcon=0.2, gbsa=1,
cut=15.0,
tempi=270, temp0=270,
dt=0.002, nstlim=200,
ntpr=100,ntwx=100,ntwr=100,
numexchg=2250,
Could you please give me any suggestions?
Atsutoshi
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Received on Sun Jul 16 2006 - 06:07:05 PDT
