On Thu, Jul 11, 2013 at 12:44 AM, Sindrila Dutta banik <
sindrila.duttabanik.yahoo.com> wrote:
> Dear all,
>
> I am trying to do umbrella sampling considering two reaction coordinates:
> increase one N-H bond length (from 1.1A to 1.8A) and decrease one O-H bond
> (from 1.8 to 1.1A) (which are part of the substrate PPD). To do the same I
> use the following input for equilibration step.
>
Is this part of a proton transfer in which one bond breaks while another
forms? If not, what are you trying to learn?
>
> 10 ps equilibration run
> &cntrl
> imin = 0,
> irest = 0,
> ntx = 1,
> ntb = 1,
> ntc = 2,
> noshakemask = ":PPD"
> ntf = 2,
> cut = 10,
> tempi = 300.0,
> temp0 = 300.0,
> ntt = 3,
> gamma_ln = 1.0,
> nstlim = 10000, dt = 0.001
> ntpr = 100, ntwx =100, ntwr =200
> nmropt = 1, ioutfm=1
> /
> &wt
> type='END',
> &end
> DISANG=comb7
>
> The comb7 file:
>
> Two restraints N-H and O-H
> &rst
> iat=12230,12245
> r1=0.0, r2=1.7, r3=1.7, r4=10.0,
> rk2=1000, rk3=1000
> &end
>
> &rst
> iat=12219,12245
> r1=0.0, r2=1.2, r3=1.2, r4=10.0,
> rk2=1000, rk3=1000,
> &end
>
> When I increase N-H bond length from 1.1 upto 1.6, there was no problem.
> When I set it 1.7 as given in the above input file it gives the following
> error.
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 3 4945 10018 10019
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
>
You cannot make or break bonds using a force field. You need to treat a
reacting center with some type of QM method. You should look at atoms
10018 and 10019 in your system to see if you can figure out why SHAKE may
be failing. If Amber is trying to SHAKE the bonds you're modifying with
harmonic potentials (which I suspect is happening), this would easily
explain your error.
That said, what your input files are doing doesn't make too much sense to
me (for the reasons mentioned above)...
Also, the usual debugging information here still applies -- try printing
out every step (coordinates, energies, velocities, anything you need) to
isolate the exact step where things break. Such an approach will often
yield insight into why a problem is occurring (and possibly even how to fix
it).
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Jul 11 2013 - 10:30:03 PDT
