[gmx-users] editconf

[Kay Gottschalk]

Works, thanks!
K.

On Feb 19, 2004, at 5:16 AM, Tsjerk Wassenaar wrote:

>
> Hi Kay,
>
> If you use -center 0 0 0 it will be centered around the origin, so it 
> will be positioned at the corner of the box. However, since you pbc it 
> shouldn't matter at all. It is mainly for visualization that you would 
> want to center, and it may decrease jumping across box borders during 
> simulation. If you really want to have it centered:
>
> editconf -f input.pdb -d 0.8
> editconf -f out.gro -o centered.pdb -center box[x]/2 box[y]/2 box[z]/2
>
> box[x], box[y] and box[z] are the first three numbers at the end of 
> out.gro
>
> Cheers,
>
> Tsjerk
>
> Kay Gottschalk wrote:
>
>> I don't know if I am doing it correctly: I centered my molecule wit 
>> editconf -f input.pdb -center 0 0 0 -o centered.pdb, then tried to 
>> build the box around it with editconf -f centered.pdb -d 0.8 -center 
>> 0 0 0. Still it doesn't seem to be centered. It is important that 
>> it's centered? Since we pbc, it should make no difference, I think...
>> Thanks,
>> Kay.
>>
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>
>
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