RE: maximum number of atoms per patch

From: JC Gumbart (
Date: Sun Feb 27 2011 - 12:34:36 CST

The command "twoAwayX yes" (same for Y and Z) will double the number of
patches. Trying to run 3.5 million atoms on only 16 processors is asking a
lot of NAMD though.

-----Original Message-----
From: [] On Behalf
Of Branko
Sent: Sunday, February 27, 2011 12:22 PM
To: namd-l
Subject: namd-l: maximum number of atoms per patch


I have a big water cluster (~ 3.5 million atoms) and try to minimize whole
system. NAMD 2.7 runing under Linux on 16 procesors (two nodes), after
proper initiation of simulation, next error could be found in out file and
simulation is disrupted: "FATAL ERROR: patch has 187437 atoms, maximum
allowed is 65535". Any suggestion is welcomed. namd file is attached.


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