Re: DCD file doubles a monomer

From: JC Gumbart (
Date: Tue Feb 26 2013 - 19:50:08 CST

I bet your cellBasisVectors are wrong. Check the dimensions of your system.

On 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

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