From: Chandra Ramananjara (
Date: Tue Aug 05 2008 - 09:27:12 CDT

Hi all,
I am writing to report a problem I'm having with NAMDENERGY. I am using NAMDENERGY to calculate interaction energies in every frame of a trajectory I have. Since the interacting atoms (between which energies are calculated) are different for each frame, I have to run NAMDENERGY once for each frame, so over the course of my 12000 step trajectory, NAMDENERGY is repeatedly called 12000 times. I've noticed that sometimes it crashes and gives a strange error. This error is of the form:

error deleting "namd-temp.*": no such file or directory,

where "namd-temp.*" is any of the temporary files used by NAMDENERGY (i.e. namd-temp.namd, namd-temp.dcd, namd-temp.pdb, namd-temp.log, etc.). There's no rhyme, reason, or pattern to this error, it occurs completely randomly, after running fine for hundreds or thousands of iterations. The files involved in the errors are also random, but it's always one of the namd-temp.* files.

I've been trying to figure out how or why this error occurs and what makes it so difficult to figure out is that it occurs so randomly. My best reason for it is that I run NAMDENERGY too many times. Most people who use NAMDENERGY usually run it just once for a whole trajectory since the groups of atoms they're calculating energies between are the same for all frames of the trajectory. For my system, the interacting atom groups vary from frame to frame so I have to run NAMDENERGY once for each frame, instead of once for the whole trajectory. Has anyone encountered this error ?