Re: [AMBER] Error in themodynamic integration with PMEMD.CUDA

From: David A Case <david.case.rutgers.edu>
Date: Thu, 21 Nov 2019 14:53:55 -0500

On Fri, Nov 22, 2019, HOCHEOL LIM wrote:

>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 think that people on the list can improve (much) on the detailed
message given above.
>
>What should I do for simulating the system with pmemd.cuda ?

Run the equilibration on the CPU until the density is stabilized. Then
switch to the GPU.

Be aware that there is a minimum system size that can be run on the GPU.
If you have only a tri-peptide, you would need a lot of solvent around
it to meet the minimum size requirements. pmemd.CUDA will tell you if
things are too small, unless you are using an old version of Amber.

....dac


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Received on Thu Nov 21 2019 - 12:00:02 PST
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