AMBER Archive (2009)

Subject: [AMBER] AmberTools and ptraj clustering on Mac OS X

From: David Watson (
Date: Sat Jan 24 2009 - 15:41:04 CST

This is a note for those who may have downloaded the (open source!)
AmberTools and compiled them to run on Mac OS X.

Clustering with ptraj can potentially create many files.
The number of "open files" in the bash shell is configured to be 256
by default.
If ptraj attempts to create more clusters than this, then you will run
into a Bus Error in the ptrajOutputCoordinates() routine.
To solve this problem, you may set the limit higher using the "ulimit"
command, e.g.:
    ulimit -n 512

If you run into this problem on a regular basis you may want to put
the ulimit command in your ~/.bashrc file.

David Watson  Graduate Student  Medicinal Chemistry  425 Faser Hall  
 University MS  38677  1.662.915.1663

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