> On Sep 30, 2016, at 7:42 AM, Elisa Pieri <elisa.pieri90.gmail.com> wrote:
>
> 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 :) )?
It may have blown up. If it dies almost immediately on the GPU, I suggest trying with the CPU and see if you get a more sensible error message.
HTH,
Jason
>
> 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 - 05:30:03 PDT
