AMBER Archive (2009)

Subject: RE: [AMBER] reg.targeted molecular dynamics

From: balaji nagarajan (balaji_sethu_at_hotmail.com)
Date: Wed Feb 25 2009 - 03:18:10 CST

Dear Amber ,

I tried Targeted Molecular Dynamics
by giving the mask to all the atoms
and i gave all the atom flags in the input
the total number of atoms are 1296
but when i run the script it shows
only 1062 atoms matches

my input file is as follows

  &cntrl
  imin = 0,
  irest = 0 ,
  ntb = 0,
  ntxo = 1,
  ntx =1,
  tempi =300.0
  ntb = 0,
  ntc=2,
  ntr =0,
  ntf = 2,
  igb = 1,
  nscm = 100,
  ntwr = 1000
  ntpr = 100,
  ntwx = 100,
  ntwv =100,
  ntwe = 100,
  ntt = 3,
  gamma_ln = 1.0,
  temp0 = 300.0
  nstlim = 10000,
  dt = 0.001,
  cut = 999,
  itgtmd=1,
  tgtrmsd =0.5 ,
  tgtmdfrc = 10.0,
  tgtfitmask= ":1-40 @ P,O1P,O2P,O5',C5',C4',O4',C1',C6,C5,C2,O2,C4,C3',C2',O3',H5T,1H5',2H5',H4',H1',N1,C6,H6,H5,N4,1H4,2H4,N3,H3',1H2',2H2',N9,C8,H8,N7,O6,H1,N2,1H2,2H2,C7,1H7,2H7,3H7,O4,H3,N6,1H6,2H6,H2,H3T,Na+",
  tgtrmsmask= ":1-40 @ P,O1P,O2P,O5',C5',C4',O4',C1',C6,C5,C2,O2,C4,C3',C2',O3',H5T,1H5',2H5',H4',H1',N1,C6,H6,H5,N4,1H4,2H4,N3,H3',1H2',2H2',N9,C8,H8,N7, O6,H1,N2,1H2,2H2,C7,1H7,2H7,3H7,O4,H3,N6,1H6,2H6,H2,H3T,Na+",
/

and the run got stopped with the error
--------------------------------------------
vlimit exceeded for step 34; vmax = 20.9476

     Coordinate resetting (SHAKE) was not accomplished
     within 3000 iterations

     Note: This is usually a symptom of some deeper
     problem with the energetics of the system.
----------------------------------------------------------------------
Is there any problem in the mask atom flags !

what does this error mean !

thanks in advance
balaji
UOM

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