Re: Strange behavior of NAMD 2.7b1

From: Axel Kohlmeyer (
Date: Wed Jan 13 2010 - 13:22:13 CST

On Wed, Jan 13, 2010 at 1:25 PM, Alexandre Suman de Araujo
<> wrote:
> 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?

yes. this is neither a bug nor a real limitation of sorts. it just is
what it is.
your system has shrunken a lot, and thus the patch grid cell lists
would have to be recomputed. NAMD does not do this automatically,
since it is effectively the same as restarting the calculation. so you
get a message like you saw and then NAMD aborts. just make sure
that in scenarios like this (i.e. at the beginning of an equilibration), you
write restarts often or run only small chunks of trajectory and then
restart repeatedly, until the system cell is closer to equilibrium size.
then this message won't show up.

> 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.

this message has been discussed on this mailing list many, many times.

the message NAMD prints out is the proper summary of what you should do.


> Cheers
> --
> **************************************************************
> Alexandre Suman de Araujo                                    *
> Faculdade de Ciências Farmacêuticas de Ribeirão Preto        *
> Universidade de São Paulo                                    *
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> **************************************************************

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.

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