[gmx-users] inquiring for solving trjconv problems

[Mehdi Bagherpour]

I am so grateful for your help
sincerely


On Mon, Jan 21, 2013 at 5:24 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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