AMBER Archive (2007)

Subject: AMBER: QM/MM Umbrella sampling

From: Jason DeChancie (jdechanc_at_chem.ucla.edu)
Date: Fri Apr 27 2007 - 15:53:08 CDT

Using Amber 9, I'm trying to run an umbrella sampling calculation with
a combined QM/MM potential for a reaction along a carbon-carbon bond.
Here is an example of an input file for one window:
  &cntrl
   imin = 0, irest = 1, ntx = 7,
   ntb = 2, pres0 = 1.0, ntp = 1,
   taup = 2.0,
   cut = 12, ntr = 0,
   ntc = 2, ntf = 2,
   tempi = 300.0, temp0 = 300.0,
   ntt = 1, tautp = 1.0,
   nstlim = 50000, dt = 0.001,
   ntpr = 100, ntwx = 100, ntwr = 100,
   ifqnt=1, nmropt=1
/
  &qmmm
   qmmask=':187',
   qmcharge=-2,
   qmtheory=2,
   qmshake=0,
   qm_ewald=1, qm_pme=1
/
&wt type='DUMPFREQ', istep1=100 /
&wt type='END' /
DISANG=c_c-11.RST
DUMPAVE=am1_c_c_vs_t.11

were the restrain file c_c-11.RST reads: &rst iat=3135,3144, r1=1.0,
r2=2.3, r3=2.3, r4=4.0, rk2=100., rk3=100., /

My question pertains to the restraint file. Are these reasonable
values for r1 and r4 to obtain a harmonic biassing potential, with a
minimum of 2.3 Å. Is the force constant defined here as 2 X 100 = 200
kcal mol-1 Å-2?

Thanks!

Jason DeChancie

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