I don’t know what you are running, of course, though from previous experience with similar issues I have two suggestions
Try to reconstruct the system, if possible, and make sure that you don’t have to much dead-space nor to little since both of these things can be issues while equilibrating
Check the parameters of your structures, due to a parameterisation issue a few years ago I had a structure “chasing its own tail”, accelerating until the simulation halted.
Best regards
// Gustaf
> On 18 Dec 2018, at 07:01, Nisha Amarnath Jonniya <phd1601271002.iiti.ac.in> wrote:
>
> 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 - 23:30:01 PST
