VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Nov 01 2007 - 17:39:14 CDT

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
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
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