From: Josh Vermaas (joshua.vermaas_at_gmail.com)
Date: Fri Aug 07 2020 - 13:46:30 CDT
Are you running with an anisotropic barostat? That is usually the problem
for oddly shaped boxes, since flexible cells can vary a lot along the short
dimensions and break NAMDs domain decomposition scheme.
Josh
On Fri, Aug 7, 2020, 12:35 PM Raman Preet Singh <ramanpreetsingh_at_hotmail.com>
wrote:
> Dear All,
>
>
>
> I am trying to simulate a linear protein fragment in water box. Using the
> solvate module in VMD, I generated a water box measuring 238x45x45 A. I
> have followed the steps mentioned in NAMD tutorial (Ubiquitin in water box).
>
>
>
> After a minimization of 10000 steps, production run of 10 ns follows.
> However, after 1000 steps of the production run, the following error occurs:
>
> FATAL ERROR: Periodic cell has become too small for original patch grid!
> Possible solutions are to restart from a recent checkpoint, increase
> margin, or disable useFlexibleCell for liquid simulation.
>
>
>
> The conf file is attached for your reference.
>
>
>
> I tried increasing minimization to 25000 steps but the error still appears
> in production run after running for a few thousand steps. Manually changing
> PMEGridSizeX/Y/Z offered no advantage.
>
>
>
> When I increased the water boxsize to 235x235x235 A and minimize for 10000
> steps, the simulation runs fine.
>
>
>
> My question is: is this error occurring due to the shape of box (a long
> cuboid compared to a near cubic box usually employed)? The bigger boxsize
> has resulted in several fold increase in number of water molecules
> resulting in a painful increase in runtime.
>
>
>
> Please help resolve the issue.
>
>
>
> Thanks!
>
>
>
> Raman
>
>
>
>
>
>
>
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