[gmx-users] box dimension
ndhumal at andrew.cmu.edu
Tue Oct 18 02:48:27 CEST 2011
I used -pbc nojump to remove pbc effect.
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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