Re: DCD file doubles a monomer

From: Aron Broom (
Date: Tue Feb 26 2013 - 12:34:54 CST

First: you can't delete things out of the coordinate (PDB file) without
remaking the topology (PSF file), so that part will never work.

In terms of the atom problem, it sounds like you have something wrong with
your periodic boundaries, and one molecule is being wrapped on top of
another. How have you set the cellBasisVector values in the namd config
file? And what are the total dimensions of your PDB file (min and max X,
Y, Z)?


On Tue, Feb 26, 2013 at 1:13 PM, Patricia Campbell <> wrote:

> Hello,
> 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
> 706-577-3754

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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