AMBER Archive (2007)

Subject: AMBER: equilibration

From: Urszula Uciechowska (urszula.uciechowska_at_pharmazie.uni-halle.de)
Date: Wed Dec 12 2007 - 11:08:00 CST


Dear Amber users,

I am trying to simulate protein model. I minimized the system and then slowyl with restraints on
the bacbone atoms I heated up now I would like to do the equilibration step.
I made this input file.

pressure equilibration
 &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 = 300.0, temp0 = 300.0,
  ntt = 3, gamma_ln = 1.0,
  nstlim = 250000, dt = 0.002,
  ntpr = 200, ntwx = 200, ntwr = 200
  
>>>restraintmask=':1-255_at_CA,C,N', restraint_wt=,

I dont have much experiences, so maybe someone could tell me if this input good or maybe I
should change or add something, what about the restraints should I include it also in this step?

thank you for any help
 

Best Regards,
Urszula Uciechowska

MSc.PhD Student
Medicinal Chemistry Group
University of Halle-Wittenberg
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