Hi Jason,
Thanks for your suggestions, I removed the restraint and everything went
fine.
Regards
Kshatresh
On Wed, Dec 31, 2014 at 1:03 AM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Tue, Dec 30, 2014 at 12:32 PM, Kshatresh Dutta Dubey <
> kshatresh.gmail.com
> > wrote:
>
> > 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
> >
>
> This restraint weight is WAYY too strong. Consider values at least 2 (if
> not 3) orders of magnitude smaller than this. And if possible, don't use
> positional restraints during your steered MD simulations.
>
> 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.
> >
>
> I would also suggest looking at the output file for any hints about what
> may have gone wrong. If you don't get any hints there, print out every
> step to see if you can catch the problem happening that way. Problems with
> SCF convergence may be due to large forces and strained calculations or a
> bad choice for the QM region (there are certain bonds, that you should
> never cut along the QM/MM boundary, like amide bonds, I think).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
With best regards
************************************************************************************************
Kshatresh Dutta Dubey
Post Doctoral Researcher,
Lise Meitner Center for Computational Quantum Chemistry
Hebrew University of Jerusalem Israel
Jerusalem, Israel
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Received on Wed Dec 31 2014 - 04:30:02 PST
