[gmx-users] Periodic Images - clarification

[Kavyashree M]

Dear Sir,

I did use dodecahedron cell.

On Mon, Jun 27, 2011 at 12:35 AM, Tsjerk Wassenaar <tsjerkw at gmail.com>wrote:

> Hey,
>
> Maybe I missed this, but what type of unit cell did you use? You
> should use a rhombic dodecahedron.
>

I did use dodecahedron cell.  but how does using a dodecahedron cell
be advantageous than any other cell when minimum image violation
has occurred? This is just my inquisitiveness. And when I was visualizing
the trajectory in VMD along with other periodic images in +/-X, +/-Y and
+/-Z
directions I saw only 26images, this is good for a cubic cell. But how
can I visualize a dodecahedron cell? Which has more faces ---> more periodic
images (If I am not wrong) than a cubic or rectangular cell..

Then, I would argue that it isn't necessarily so problematic as the
> others put it when you have transient contacts. For the greater part
> of the simulation the distances in the periodic system are so large
> that there can be no direct effect between opposite ends of the
> protein. It is unlikely that the brief periods where the opposite ends
> were within each others sphere of influence - not in contact - would
> have caused a persistent deviation from in ensemble. Mind that it's
> not wrong that a protein would suddenly feel some presence from some
> end of a similar protein some distance away at some time. It's just
> wrong if a protein aligns with itself. That has not happened if these
> minimal distances were only transient. It may well be that the protein
> was going from one conformation to another, for which it had to go
> through something that would violate the PBC a bit. Still, you are in
> for some discussion, and have to argue, based on what the simulation
> shows you, what (a) replicate simulation(s) show(s) you and what you
> know of your protein, why it would be justified to draw conclusions
> based on that trajectory.
>
> But those are just my two cents.
>

Thanks for the suggestions sir. I will be verify this with the dimer
(disulphide
bonded) and monomer in a larger box size.

Thanking you
With Regards
M. Kavyashree
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