VMD-L Mailing List

From: Θωμας Ευαγγελιδης (te8624_at_mbg.duth.gr)
Date: Mon Aug 20 2007 - 16:25:33 CDT

Hi,
I have written a plugin for VMD (~320 lines of code) which creates smaller dcd
and psf files from bigger ones by taking into account only the atoms that are
within $cutoff distance from the macromolecule. The program works fine with a
small number of frames, but when this number exceeds 10 it crashes. At first I
thought that there was a memory leak so I filled up the program with unset
commands, but the problem still remained. After that I split it in 2 parts. The
first produces the "truncated frames" in pdb format, and the second finds which
atoms must be included in each one in order the final frame-pdbs to contain the
same intact residues and the same atoms. The program works by creating,
concatenating and deleting many pdbfiles. I tried to run the first part, close
the VMD, restart it and run the second, but the program always crushed at the
same point of the second part. In example when I used 11 frames it crashed at
frame 10, and when I
used 15 frames from the same initial dcd it crashed at frame 8.
Does anyone has any idea about what is going wrong? I could send the code if
that would help.

Thomas