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
Received on Tue Dec 30 2014 - 15:30:02 PST
