VMD-L Mailing List

From: Maria Bagonis (mbagonis5_at_googlemail.com)
Date: Thu Nov 01 2007 - 16:11:04 CDT

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