# [AMBER] Temperature and TI with qm/mm

From: Fabrício Bracht <fabracht1.gmail.com>
Date: Sat, 9 Nov 2013 05:33:09 -0200

Hi, after much hard work and several failed attemps I have finally been
able to set a TI calculation with qm/mm (DFTB) to work. After getting rid
of the vlimit problems and SCF convergence problems on V1, now I have one
final problem that I can't seem to get rid of. This TI simulation is a
continuation of a classical TI simulation. I figure that the
pre-equilibrated structure from a certain lambda value would be the best
structure to continue the simulation, bu now using qm/mm. The problem is
that the temperature of the system falls from the previous 298K to around
213 K and it stays like that for as long as I have simulated.
Here is the input for v0:
polyA-polyT 10-mer: 20ps MD with res on DNA
&cntrl
imin = 0,
irest = 1,
ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1, taup = 2.0,
cut = 8.0,
ntr = 0,
ntc = 2,
ntf = 1,
tempi = 298.0,
temp0 = 298.0,
ntt = 3,
gamma_ln = 10.0,
nstlim = 250000, dt = 0.001, ntave = 100,
ntpr = 10, ntwx = 100, ntwr = 10,
ig = -1, ioutfm = 1, iwrap = 1,
icfe = 1, ifsc = 1, clambda = 0.01592,
noshakemask = '', scmask = ':342', idecomp = 1, nmropt = 0,
ifqnt=1, nmropt = 0,
/
&qmmm
qmcharge=-1,
dftb_3rd_order = 'PA',
printcharges = 1,
qm_theory='DFTB',
qmshake=0,
qm_ewald=1, qm_pme=1
qmcut=12.0,
/
Receptor residues
RRES 1 7102
END
Printing
RES 1 342
END
END

Everything is all right, both energetically and structurally. The really
strange thing is that the kinetic energy is almost the same as it was with
the classical simulation, around 20000. The volume is also similar, but the
temperature now reads around 213.
Any ideas to what might be going on?
Thanks
Fabrício
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Received on Sat Nov 09 2013 - 00:00:02 PST
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