Dear Sir
wish you are fine !
I need to run MD simulation on a small constant volume periodic box
containing only a crystal of a protein without any solvation. However, when
minimizing the structure, I had a problem with the cut of . the cut off
needed to be very small about 1 Angstrom and the minimization was not able
to run without higher or lower values of cut off . with the following
control file
imin.in
&cntrl
imin=1, ntmin=2, maxcyc=5000, nmropt=0,
ntx=1, irest=0,
dx0=0.0010, drms=0.00010,
ntxo=1, ntpr=100, ntrx=1, ntwr=100,
iwrap=0, ntwx=100, ntwv=0, ntwe=0,
ioutfm=0, ntwprt=0, idecomp=0,
ntf=1, ntb=1, igb=0,
cut=1, Tol=.00001
ntc=1, jfastw=0,
ibelly=0, ntr=0
&end
and even with this
I got the following
NSTEP ENERGY RMS GMAX NAME NUMBER
1 2.7987+247 Infinity 1.5160+249 CA 60
BOND = 54.6193 ANGLE = 209.7600 DIHED =
497.3500
VDWAALS = -33641.9663 EEL = ************* HBOND =
0.0000
1-4 VDW = 217.6989 1-4 EEL = 2924.5790 RESTRAINT =
0.0000
what should I do to fix this error ? all the information of how I prepared
the crystal is available upon request .
Regards
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Received on Thu Oct 15 2015 - 00:30:02 PDT
