Do you get the error right away? If not, which step does the error
occur at? Do you get any enormous or '****' energies? You should set
'ntpr' to something much smaller (say 10 or even 1) in order to debug.
Also, your restraint weight is insanely high - 10000 is orders of
magnitude larger than you need. Try something like 5 or 10 instead.
-Dan
On Fri, Apr 7, 2017 at 3:44 AM, Sadegh Faramarzi Ganjabad
<safaramarziganjabad.mix.wvu.edu> wrote:
> Hello,
>
> When I restart simulations of a system with restrained backbone atoms I get
> the following error
>
> 'ERROR: Calculation halted. Periodic box dimensions have changed too much
> from their initial values.
> Your system density has likely changed by a large amount, probably from
> starting the simulation from a structure a long way from equilibrium.
>
> [Although this error can also occur if the simulation has blown up for
> some reason]
>
> The GPU code does not automatically reorganize grid cells and thus you
> will need to restart the calculation from the previous restart file.
> This will generate new grid cells and allow the calculation to continue.
> It may be necessary to repeat this restarting multiple times if your
> system
> is a long way from an equilibrated density.
>
> Alternatively you can run with the CPU code until the density has
> converged
> and then switch back to the GPU code.'
>
> I doubt it is because of the periodic box, since when I restart the same
> simulation without turning restraints on it works fine. Also, the density
> doesn't change a lot, and I am restarting calculations from the previous
> restart file. The error is similar to my previous post, except this time I
> switched 'iwrap=1' off. Is there anything I can do to solve the issue? I am
> also copying my config file here.
>
> Thanks,
> Sadegh
>
>
> &cntrl
> irest=1, !
> ntx=5, !
> imin=0, ! (no minimization)
> ntr=0, !
> ntf=2, ! (Force evaluation,complete interaction is calculated)
> ntc=2, ! (SHAKE,bonds involving hydrogen are constrained)
> tol=0.0000001, ! (shake tolerance)
> cut=12.0, !
> fswitch=10.0,!
> ntt=3, ! (Langevin dynamics for temperature control)
> ig=-1, ! random seed
> gamma_ln=5.0, ! (collision frequency)
> temp0=310.0, ! (reference temperature)
> ntp=1, ! ( pressure control, isotropic (x-,y-,z-) pressure
> scaling)
> ntb=2, ! (constant pressure (default when ntp > 0))
> taup=8.0, ! (Pressure relaxation time)
> ntpr=5000, ! (print energy output interval)
> ntr = 1, ! Turn on positional restraints
> ntrx =1,
> restraint_wt = 10000, ! 10 kcal/mol/A**2 restraint force
> constant
> restraintmask = '.CA,C,O,N' ! Restraints on the backbone atoms only
> ntwr=5000, ! (frequency to write restart file)
> ntwe=0, ! (don't write energies and temperature to mden file)
> ntwx=5000, ! (write coordinates to the mdcrd file)
> nstlim=10000000, ! (Number of MD-steps. 90ns, total of 100ns)
> dt=0.001, !
> /
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 07 2017 - 06:30:03 PDT
