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Re: possible minimum box size

From: Jean-Noël Grad
Subject: Re: possible minimum box size
Date: Tue, 01 Mar 2022 02:36:28 +0100
User-agent: Roundcube Webmail/1.3.17

Hi again,

Sorry, I forgot to mention that the error message "number of cells 1 is smaller than minimum 8" is typically emitted on 1 MPI rank when the system contains a bond whose cutoff is larger than half the max interaction range calculated with the formula in my last email (or larger that one quarter if a dihedral is present).


On 2022-03-01 01:03, Jean-Noël Grad wrote:
Dear Ahmad Reza,

The minimum box size can be calculated with the following formula:

max_interaction_cutoff = min(system.box_l /
system.cell_system.node_grid) - *
(system.cell_system.get_state()['n_nodes'] > 1)

If your polymer has dihedrals, divide this value by 2. Run the
attached MWE with 1 or 2 MPI ranks to see the effect of the LJ cutoff
and skin.


On 2022-02-28 16:15, Ahmad Reza Motezakker wrote:
Dear EspressoMD users,

I have a system including 2 polymer chains. In the warm up stage, I
face below error:

Encountered errors during integrate: ERROR: number of cells 1 is
smaller than minimum 8 (interaction range too large or min_num_cells
too large)

The polymers are made of 15 beads (sigma = 1). cut off radius is
2**(1/6). I have played with box size and skin and cut off to see what
is happening but it only works with box size of 57. Could you please
help me with that? I want to decrease the box size to the smallest
possible size.

Thank you very much,

Ahmad Reza

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