Dear Amber Users,
When I was running the density equilibration of a protein, calculations
terminated at Nstep=12500 and I got this message "Nonbond cells need to be
recalculated, restart simulation from previous checkpoint. with a higher
value for skinnb". What is skinnb? Has anyone come across this problem
before? The input follows:
&cntrl
imin=0,irest=1,ntx=5,
nstlim=1000000,dt=0.002,
ntc=2,ntf=2,
ntb=2, ntp=1, taup=1.0,
ntpr=500, ntwx=500,
ntt=3, gamma_ln=2.0,
temp0=300.0,
ntr=1, restraintmask=':1-106',
restraint_wt=2.0,
/
The minimization of this structure showed the "RESTARTED DUE TO LINMIN
FAILURE" message but it finished normally. This seems like a common error
occurred in minimization and it wouldn't affect running MDs, but did it
cause the above "skinnb" problem?
Thanks for helping!
-RIchard
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Received on Mon Jun 17 2013 - 15:30:02 PDT
