Re: DCD file doubles a monomer

From: Patricia Campbell (
Date: Tue Feb 26 2013 - 12:13:53 CST


In combination with the 'DCD file doubles a monomer' 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.

On Tue, Feb 26, 2013 at 1:09 PM, Patricia Campbell <> wrote:

> Hello,
> 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.
> --
> Patricia Campbell
> 706-577-3754

Patricia Campbell

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