[gmx-users] box dimension
Mark.Abraham at anu.edu.au
Tue Oct 18 03:18:23 CEST 2011
On 18/10/2011 11:48 AM, Nilesh Dhumal wrote:
> I used -pbc nojump to remove pbc effect.
Please read trjconv -h about -pbc nojump. If molecules can't jump, then
they must diffuse. You can't have both.
> trjconv 3.trr -s 3.tpr -pbc nojump -o 500-11.pdb
> Basically I want to find the conformer close to center of box.
> On Mon, October 17, 2011 6:36 pm, Mark Abraham wrote:
>> On 18/10/2011 7:05 AM, Nilesh Dhumal wrote:
>>> I have saved the coordinates of snapshot from trajectory in pdb file.
>>> The dimesnion of box in pdb file are
>>> 32.805 32.805 32.805 90.00 90.00 90.00 P 1
>>> I am trying to find atoms close to center of box.
>>> there are atoms whose distance from center is more that ~17 A. My
>>> center coordinates are 0.0 0.0 0.0.
>>> How is it possible?
>> Molecules diffuse across periodic boundaries during the simulation.
>> While computing interactions, mdrun corrects for periodicity on the fly,
>> but does not trouble itself to guess what manner of post-processing you
>> would like to do. There is a suggested trjconv workflow on the the GROMACS
>> website. I suggest you try it.
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