[gmx-users] inquiring for solving trjconv problems

[Justin Lemkul]

On 1/20/13 8:34 PM, Mehdi Bagherpour wrote:
> excuse me Dear Justin
>
> I could not understand exactly what to do?
> My simulation system is DNA in water.
>

The -center option is convenient when you have to center a single molecule 
within a unit cell.  If you have two molecules or more that you wish to center, 
it can be more complex than you might expect.  Consider the following boxes. 
Both represent a double-stranded DNA molecule that is considered centered in the 
box:

  __________
|          |
|          |
|    XX    |
|          |
|__________|

  __________
|          |
|          |
X          X
|          |
|__________|

In both cases, the geometric center coincides with the center of the box, even 
though the two molecules are split via PBC.  My previous suggestion (and there 
are more detailed examples of what to do by reading the wiki site and checking 
the mailing list archive) is to make an index group that represents a more 
well-defined center.  In the case of a protein dimer, maybe this would be a few 
residues that are at the protein-protein interface, thus enforcing a more strict 
criterion for centering.  For a DNA molecule, maybe center on only one strand, 
such that the other strand is repositioned based on a more intuitive reference. 
  Even centering on a single nucleotide would probably work.  Otherwise, trjconv 
has a variety of options (again, check the wiki for a workflow) that can deal 
with these situations.  Often times, a single command is insufficient to achieve 
the representation you want.  Other options like -fit could also be useful here, 
but not in conjunction with -pbc.

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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