Thank you Jason and David,
I used the inputs at
http://jswails.wikidot.com/explicit-solvent-constant-ph-md; anyway, even if
the minimization and heating look fine, during the equilibration I get:
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 don't really get what "you will need to restart the calculation from the
previous restart file" means..because what I understand is either "restart
from the heat.rst7", which of course does not make sense, or "restart from
the equil.rst7", which, in my case is unfortunately empty, since the error
occurs almost at the beginning of my simulation.
Should I just switch to the CPU code? Or there is some other problem (and a
solution :) )?
Elisa
On Thu, Sep 29, 2016 at 8:53 PM, David A Case <david.case.rutgers.edu>
wrote:
> On Wed, Sep 28, 2016, Elisa Pieri wrote:
> >
> > I have a PDB containing a protein inserted in a membrane, plus two water
> > layers, yielding a "cubic" unit. Here the tleap input I used to get the
> > parameters:
> >
> > source leaprc.constphRET (<-- a customized leaprc for the cromophore)
> > source leaprc.lipid14
> > loadAmberParams frcmod.ionsjc_tip3p
> > monomer = loadPDB monomer.pdb
> > setBox monomer "vdw"
>
> Are you sure you want this command? Don't you already know the size of the
> box to use? If so, replace the above with this:
>
> set monomer box { a b c}
>
> where a b c are the sizes of the box in your model. Then, as Jason said,
> use periodic boundary conditions at all stages of subsequent calculations.
>
> ....good luck....dac
>
>
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Received on Fri Sep 30 2016 - 05:00:02 PDT
