NAMDenergy: does rewrite temp files at different timesteps

From: Neelanjana Sengupta (
Date: Fri Aug 07 2009 - 00:18:14 CDT

Hi all,

I have written a tcl script using NAMDenergy to calculate the nonbonded
energies bewteen 2 evolving selections at every timestep. This is how my
script works:
i) Load a single frame
ii) Make the two selections (these are somewhat complicated and depend on
another calculation, hence a simple update at each step won't work).
iii) Calculate energies (these are const. energy trajectories. Since the
cell doe snot fluctuate, the -extsys nve.xsc works with any timestep)
iv) Delete the molecule
v) Load the next frame and begin from (i) again.

Now, this worked well for one of my simulations (the results are meaningful
too). However, for another system (which just happens to have a greater
number of solvents), NAMDenergy reports a Segmentation Fault, apparently
happens because it cannot write a namd-temp.pdb file (since I don't use
-debug, the temp files are getting deleted after each calculation).
Interestingly, this happens at *different points *when the same script is
run multiple times!

I have also tried using a variable ( say 'count') which changes at each
step, ie. I use -temp $count to write out files with different names. This
did not help.

Can I get some advice on how to get over this problem?

Thanks a lot,
Neelanjana Sengupta


This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:53:08 CST