Periodic cell too small with GPUs, not with pur CPUs

From: Francesco Pietra (
Date: Wed Jul 05 2017 - 02:09:14 CDT

I am at an unbiased MD with a large protein containing organic ligands in a
TIP3P box that (wrapall on) gave no troubles on a Nextscale cluster on 264
pure CPUs along a 58.2ns simulation, ts=1.0fs.

On trying to continue the simulation with my workstation with a couple of
GTX680, I am facing immediate "periodic cell became too small" under either
"wrapall on" or "wrapall no" (I used successfully this hardware for MD up
to this case). NAMD_CVS_2017-05-25_Linux-x86_64_multicore-CUDA.

In contrast, the simulation continues without problems (albeit very slowly)
on pure CPUs with a desktop, either "wrapall no" (which was the reason for
continuing the simulation in order to safely measure the distances between
the centers of mass of protein and ligands) or "wrapall on".

francesco pietra

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