Cuboid water box issues

From: Raman Preet Singh (
Date: Fri Aug 07 2020 - 13:29:06 CDT

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.



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