From: Alexandre Suman de Araujo (asaraujo_at_fcfrp.usp.br)
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.
Cheers
-- ************************************************************** 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: asaraujo_at_fcfrp.usp.br* Av. do Café, s/n° * e-mail: ale.suman_at_gmail.com * CEP: 14040-903 * Phone: +55 (16) 3602-4172 * Ribeirão Preto, SP, Brasil * Phone: +55 (16) 3602-4222 * **************************************************************
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