[AMBER] Need help in SMD

From: Kshatresh Dutta Dubey <kshatresh.gmail.com>
Date: Tue, 30 Dec 2014 19:32:34 +0200

Dear Users,

I am using SMD for bond breaking process. Firstly I did minimization using
DFTB and then heating and equlibration dynamics using QM/MM with DFTB.
After that I went for bond stretching. During SMD calculation, it runs fine
for 200 steps but stops suddenly without any error and it prints output for
SMD.txt for 200 steps. I am unable to figure out the problem. I am using
following input :

Equlibration using QM potential
  &cntrl
        imin=0, nstlim=500000,
        dt=0.002, irest = 1, ntx = 7,
        ntt=3, pres0 = 1.0, ntp = 1,temp0=300.0,
        ntb=2,taup=2.0, ntr=1, restraint_wt=1000.0
        ntf=2, ntc=2,restraintmask=':5960,6503',
        cut=8.0, gamma_ln = 2.0,
        ifqnt=1,
        ntpr = 500, ntwr=500, ntwx = 500,
  /
  &qmmm
        qmmask=':13',
        qmcharge=-1,
        qm_theory='DFTB',
        qmcut=8.0,
        writepdb = 1
  /

ncsu_smd

   output_file = 'smd.txt'
   output_freq = 500

   variable
   type = DISTANCE ! Distance
   i = (388,390)
   path = (X,5.0)
   harm = (50.0)
   end variable

end ncsu_smd

I want to vary the distance between atoms 388 and 390 by 5 angs, but it
varies only for 1.47 to 1.49 angs. These atoms belong to residue 13 which
is in QM region.
I will be very much thankful if someone helps me to run it properly. Thanks
in advance.

Regards
Kshatresh
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Received on Tue Dec 30 2014 - 10:00:02 PST
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