Dear Amber users!
I've faced with the problems during equilibration of my protein using
pmemd.cuda
1- I've started to heat my protein in nvt and quickly obtained
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.
visualization show me that individual water have been moved towards the box
boundaries being separated from the rest of the solvent.
What would be best solution here
1- Switch to the sander and perform all equilibration using cpu
2- Do equilibration using cuda starting in NPT (with frozen protein) with
applied barostat preventing such density artifacts ?
James
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Received on Mon Jun 09 2014 - 01:30:02 PDT
