Strange behavior of NAMD 2.7b1

From: Alexandre Suman de Araujo (
Date: Wed Jan 13 2010 - 12:25:49 CST

Hi all.

I'm performing a simple simulation of a POPC membrane in water. After
1000 steps of minimization I started the MD using NPT ensemble, time
step of 2 fs, pbc and PME. After 1000 steps a had the follow error:

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.

I tried a lot of solutions (changing simulation parameters) and I got
the same error. The simulations stopted to crash just after I change the
/pairlistdist/ parameter from /13.0 /to/ 14.0. /So I remembered another
simulation with this same problem and when I looked at /pairdistlist/ it
was set as 17.0. Another membrane simulations that NOT show this kind of
errors had /pairdistlist/ = 15.0.

Is this just a coincidence that the crashed simulations had pairdistlist
as prime numbers or this can be a bug or some limitation of any algorithm?

Changing /pairdistlist/ from 13 to 14 or from 17 to 16 is not a problem
to me, but if this is a (known or unknown) problem/bug I think it is
important to be discussed.


Alexandre Suman de Araujo                                    *
Faculdade de Ciências Farmacêuticas de Ribeirão Preto        *
Universidade de São Paulo                                    *
Dep. de Física e Química                                     *
Grupo de Física Biológica     * e-mail:*
Av. do Café, s/n°             * e-mail:  *
CEP: 14040-903                * Phone: +55 (16) 3602-4172    *
Ribeirão Preto, SP, Brasil    * Phone: +55 (16) 3602-4222    *

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