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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Received on Sun Apr 29 2007 - 06:07:40 PDT
