AMBER Archive (2009)

Subject: [AMBER] reg.Targeted molecular dynamics

From: balaji nagarajan (balaji_sethu_at_hotmail.com)
Date: Tue Feb 17 2009 - 23:26:49 CST

dear amber ,

I am doing TMD using amber ,
I have took two structures
and minimized them and equillibriated them
separately and with that ,
I have fixed one as the reference structure and the other as a Target ,
I have started doing TMD in vaccum .
The two structures are having same number of atoms ,
and they have a rmsd difference greaterthan 10 .
as if now I am making the input file ,
my input file is as follows

 &cntrl
  imin = 0,
  irest = 0 ,
  ntb = 0,
  ntxo = 1,
  ntx =1,
  tempi =300.0
  ntb = 0,
  ntc=2,
  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 = 10000000,
  dt = 0.001,
  cut = 12.0,
  itgtmd=1,
  tgtrmsd =15 ,
  tgtmdfrc = 1.0
  tgtfitmask= ":",
  tgtrmsmask=":"

/

i didnot gave any mask , and i want to know wether i have given the TMD flags correct ,
the two flags are confusing ,
tgtrmsd
tgtmdfrc
in the way how we have to give values for it while doing the simulation based on the two structures of interest ,

and how one can give the force to the target molecule ,

thanks in advance !
balaji
UOM

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