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

From: David A Case <>
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
> is a long way from an equilibrated density.
> Alternatively you can run with the CPU code until the density has
> 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.


AMBER mailing list
Received on Thu Nov 21 2019 - 12:00:02 PST
Custom Search