DCD file doubles a monomer

From: Patricia Campbell (patricia.campbellsoup_at_gmail.com)
Date: Tue Feb 26 2013 - 15:01:18 CST


I am trying to run a large simulation comprised of over 20 monomers (1.6
million atoms total after solvation/ionization). The simulation never makes
it past the first step of equilibration before crashing due to atom
velocity. Recently, I tried running the structure through 20000
minimization steps. I checked the structure and I noticed that the dcd file
adds a monomer on top of another monomer after the first frame. When the
equilibration crashes its due to atoms located in either of these two
monomers. The two monomers are right on top of one another. I have no idea
how this is happening. I also tried running a minimization in vacuo and the
same thing happened after the first frame. Furthermore, I tried deleting
the second monomer out of the PDB file but then was unable to load the PDB
file into the PSF file in VMD. Is there any way to stop this??? Thank you. I
have to add that when I run this simulation on 6 monomers or less this does
not happen. I need to run this larger scale simulation so that I can
monitor interactions between hexamers and pentamers (this is a part of a
capsid). Thank you.

Patricia Campbell
Patricia Campbell

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