Dear all,
Im using amber12 pmemd.cuda_SPFP( Version 12.3) to run MD simulation to
study the protein folding problem. But the running process is always
terminated soon. There was nothing error in the md2.out. The log.txt
exports: Nonbond cells need to be recalculated, restart simulation from
previous checkpoint with a higher value for skinnb.and I can not understand
what does it mean.
My input file
irest=1, ntx=5,
imin=0, ! run MD
ntb=2, ntp=1, pres0=1.0, taup=2.0, ! periodic box, constant pressure
! ntb=1, ! constant volume
ntpr=10000, ntwr=10000, ntwx=10000,
ntt=3, gamma_ln=1.0, tempi = 298.0, temp0 = 298.0,
ig=177559, ! rand number
ntf=2, ntc=2, ! SHAKE
nstlim=30000000, dt=0.001, ! steptime
cut=12.0,
iwrap=1
/
Any help will be appreciate. Thanks a lot.
Yours
Tu Zhiping
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Received on Wed Jun 19 2013 - 03:00:02 PDT
