VMD-L Mailing List

From: Maria Bagonis (mbagonis5_at_googlemail.com)
Date: Mon Nov 05 2007 - 18:23:08 CST

Thanks so much. I don't know why I didn't think to try that before. It was
very helpful.
All the Best,
Maria

On 11/1/07, John Stone <johns_at_ks.uiuc.edu> wrote:
>
>
> Hi,
> Have you tried unwrapping your trajectory using the PBCTools plugins?:
> http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Nov 01, 2007 at 05:11:04PM -0400, Maria Bagonis wrote:
> > Hi,
> >
> > I have a brief inquiry.
> > In a couple of my simulations my protein has diffused to the edge of the
> > simulation box. When this occurs one chain of the dimer wraps to
> > the opposing side of the simulation box in VMD, while the other chain
> does
> > not wrap, remaining on the side of origin. In both cases, a significant
> > portion of both peptide chains lie outside the unit cell in the VMD
> > visualization. Unfortunately, after a fairly rapid initial diffusion of
> the
> > protein in the first 300 ps of the simulation, the protein's overall
> > position in the simulation box becomes relatively stable. Therefore, it
> > becomes "trapped" in this awkward position in the cell for the remainder
> of
> > the simulation so that the 2nd peptide chain never wraps as did the
> > first. (The initial diffusion of the protein seems to be hampered when I
> > restart the simulation).
> >
> > I would like to calculate the RMSD for the entire protein, however,
> the
> > typical alignment methods provided in VMD will not work in this case,
> since
> > the protein is partitioned awkwardly within the unit cell (though I can
> > calculate RMSD for each individual chain of the protein using this
> method).
> > Has anyone encountered such a problem before? If so, any advice
> regarding
> > this matter would be greatly appreciated.
> > Thanks
> > Maria
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>