[gmx-users] center an atomic group

[Dr. Vitaly V. G. Chaban]

> On 6/21/12 3:20 PM, Dr. Vitaly V. G. Chaban wrote:
>>
>> Dear All -
>>
>> I have a macromolecule surrounded by multiple layers of water in my
>> box. For visualization purposes, I would like to center the
>> macromolecule in the box (PDB file), so that its geometrical center
>> coincides with the geometrical center of the cubic box (as
>> visualization utilities undertand this center).
>>
>> Would anyone please suggest a handy route within the gromacs utilities
>> to achieve this? I tried to use
>>
>> editconf -center $macromol_center_coords -f conf.gro -o conf.pdb
>>
>> I am not sure what it exactle does, but the macromolecule was not at
>> the center of the box.
>>
>
> In the absence of setting a box, the editconf approach may not work.  I use
> -center and -box in concert to position solutes in a box, though I don't
> know, in principle, why this doesn't work.
>
> trjconv -center is designed to do exactly what you're looking for.
>
> -Justin


Thanks Justin. trjconv -center sounds nice. I will get a try. ~Vitaly


>
> --
> ========================================
>
> 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
>
> ========================================
>
>