[AMBER] cutoff problem with a periodic crystal box

From: Hadeer ELHabashy <hadeer.elhabashi.gmail.com>
Date: Thu, 15 Oct 2015 09:26:43 +0200

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
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