Re: [AMBER] Calculation halted on pmemd.cuda

From: Carlos Simmerling <>
Date: Fri, 26 Mar 2021 21:32:29 -0400

it will help if you can say what you are simulating. this can be a common
problem where users have non-standard force field parameters and the system
becomes unstable. it also can be a problem with very strained initial
structures. Let people know how you generated your initial coordinates, and
if it is using standard parameters provided with Amber.

On Fri, Mar 26, 2021 at 8:10 PM 库米尔 <> wrote:

> Dear Amber community,
> My simulation frequently halts on cuda with the following error message
> after I have done series of minimization and equilibration of system:
> 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.
> And with little experience I have got with my system, whenever I encounter
> such errors I have to go back to the packing stage to increase the number
> of molecules/atoms in the box( undesirable) or use slow sanders to overcome
> such a challenge which admittedly is very unsustainable for the kind of
> system am dealing with. In fact it is causing me a lot of headache and
> discomfort. Is there better way to fix this challenge once and for all?
> Alex
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Received on Fri Mar 26 2021 - 19:00:02 PDT
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