[gmx-users] box dimension

[Nilesh Dhumal]

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.

Nilesh

On Mon, October 17, 2011 6:36 pm, Mark Abraham wrote:
> On 18/10/2011 7:05 AM, Nilesh Dhumal wrote:
>
>> Hello,
>>
>>
>> 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.
>
> Mark
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