RE: Incorrect atom count in binary file

From: Norman Geist (
Date: Wed Feb 18 2015 - 03:13:52 CST

There are two NAMD options that control if restart files are ascii or binary:


binaryoutput yes/no <-- controls the final restart set

binaryrestart yes/no <-- controls the intermediate restart sets


So as you are using the file *restart.coor you use a file controlled by “binaryrestart”. It assume that you have set binary restart to “no” so you would need to use





instead of:





You can check if your restart file is ascii or binary by simply doing “cat yourfile” and see if you can read the content. If it just cryptic than the file is binary and your problem is somewhere else. Maybe the file is corrupted and you may want to try the*.old restart files instead. If that also doesn’t work, you atom count is in fact different between psf and restarts and so will never work together.


Norman Geist.


From: [] On Behalf Of Mihaela Drenscko
Sent: Wednesday, February 18, 2015 2:00 AM
Subject: namd-l: Incorrect atom count in binary file



I was running several metadynamics simulations with pcl (polycaprolactone) monomers in water. I had no problem with lower number of monomers (such as 5, 10, 20, 30, 44), but with 58 monomers, the simulation stops, with the error:

Info: Reading from binary file ../../pcl58waterequi50.out.restart.coor
FATAL ERROR: Incorrect atom count in binary file ./../pcl58waterequi50.out.restart.coor

What is the cause of it and how do I fix it?

Thank you,


This archive was generated by hypermail 2.1.6 : Tue Dec 27 2016 - 23:20:54 CST