On Mon, May 15, 2023, Steinbrecher, Thomas via AMBER wrote:
>
>I see the following error message occurring seemingly at random (in about
>20% of runs) in some repeats of a large membrane system simulation (running
>Amber22 pmemd.CUDA on RHEL with ff19SB+gaff2+lipid21+OPC water):
>
>-----------------------------------------------
>ERROR: Calculation halted. Periodic box dimensions have changed too much
>from their initial values.
>------------------------------------------------
Just to check: how far into the simulation does this occur? Are you
printing often enough to be sure that you are seeing all the volume changes that
are taking place? (Especially if the error is early in the run.)
Note that vlimit is not checked on the GPU, but you can monitor the
temperature via mdout. A couple things to try:
1. Have you done enough initial NVT eqilibration before switching to NPT?
(I don't know what "enough" is here, but try 10 ns or so.)
2. Try NPT with the MC barostat to see if you get past this problem; you
can switch to the Berendsen barostat later.
Of course, it would be good if pmemd reported more details about what is
going on -- at least exactly which dimension values were involved.
....good luck...dac
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Received on Mon May 15 2023 - 05:30:02 PDT
