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
Received on Fri Apr 07 2017 - 01:00:02 PDT
