Dear AMber user,
I would like to run amd for my system containing protein, ligand, ANP and
MN. But while running 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.
#####################################################
Even I tried the last alternative by slowing heating in steps and
removing the restraint slowing and till the density convergence in CPU ,
then run its equilibration in GPU.
Please suggest.
--
Nisha Amarnath Jonniya
PhD Research Scholar
Biosciences and Biomedical Engineering
Indian Institute of Technology, Indore
India
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Received on Mon Dec 17 2018 - 22:30:02 PST
