First check the density and see if it is reasonable. It may just be a
change during equilibration as the message says. If it did get too large,
then look carefully at your modified residue. Problems in md are often
related to bad parameters, or ok parameters not properly used. It can also
be that your initial structure was poor and needs more careful
equilibration. Analyze your energies to check that.
On Mon, Apr 6, 2020, 5:12 AM Gallo, Angelo <A.Gallo.1.warwick.ac.uk> wrote:
> Dear Amber users,
>
>
>
> I was running, as most of time, a minimization with some heat steps and
> equilibration prior the production step.
>
>
>
> It is the first time I am using AMBER18 to generate the prmtop and prmcrd
> file I never experienced the error reported below.
>
> Usually I generated the prmtop and prmcrd with either Amber12 or Amber14.
>
>
>
> Just few days ago using AMBER18 on the protein in its apo form I had no
> issue, but today I had the following error on the same protein but holo. In
> this holo protein there is just a modified residue.
>
>
>
> Looking at the prmtop and prmcrd I can’t see any error if there is any
>
>
>
> It does not stop immediately I have five steps and it stops at the third
> one (sander2.in)
>
>
>
> As attached file you can find the input file I have been using.
>
>
>
> 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.
>
>
>
> Any suggestion for debugging this issue
>
>
>
> Thanks in advance
>
>
>
> Best
>
>
>
> Angelo Gallo
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>
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Received on Mon Apr 06 2020 - 04:00:01 PDT
