AMBER Archive (2008)

Subject: AMBER: Umbrella Sampling for proteins

From: German Erlenkamp (german.erlenkamp_at_pharmazie.uni-halle.de)
Date: Mon May 26 2008 - 04:23:56 CDT

Hello Amber-Users,

I want to do an umbrella sampling for a residue in my protein, but I've
got a few question how to start this:

I've got my mdin-file:
 &cntrl
  imin = 0, irest = 1, ntx = 7,
  ntb = 2, pres0 = 1.0, ntp = 1,
  taup = 2.0,
  cut = 9, ntr = 0,
  ntc = 2, ntf = 2,
  tempi = 298.15, temp0 = 298.15,
  ntt = 3, gamma_ln = 1.0,
  nstlim = 250000, dt = 0.002,
  ntpr = 200, ntwx = 200, ntwr = 200
 /
 &wt type='DUMPFREQ', istepl=10 /
 &wt type='END' /
DISANG=chi.RST
DUMPAVE=chi_vs_t.170

and the chi.RST-file:
 &rst iat=9,10,11,12,13,14, r1=0., r2=170., r3=170., r4=360., rk2=30.,
 rk3=30., /

1) Where can I find some appropriate restraints for the residue?

2) I want to separate my md in smaller parts about 500ps. So is the
DUMPAVE-file overwritten with every new start, and do I have to change
the name for every new 500ps?

Thanks for your help! 

-- 
German Erlenkamp
Institut fuer Pharmazeutische Chemie
Martin-Luther-Universitaet Halle	
Wolfgang-Langenbeck-Str.4
06120 Halle/ Saale

E-Mail:	german.erlenkamp_at_pharmazie.uni-halle.de
Phone: (49)345 - 55 25 043
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