From: Joshua . (joshua.timmons1_at_gmail.com)
Date: Wed Jul 05 2017 - 09:39:40 CDT
I am new to NAMD, but I had a similar problem "periodic cell became too
small" and resolved it by setting margin to 10 (while keeping wrapAll on).
Documentation from 2.6 says to leave it alone unless trying to optimize
performance, but it solved the issue for me immediately:
On Wed, Jul 5, 2017 at 3:09 AM, Francesco Pietra <chiendarret_at_gmail.com>
> 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
> francesco pietra
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