Hi,
Sure, that's what trjconv -pbc and -ur are used for. There's no way to ask
mdrun to automatically do the particular operation you want.
Mark
On Tue, May 29, 2018 at 3:21 PM Alex wrote:
> Hi Mark,
> Thanks.
> The problem is that only the slab shifts and water molecules stay x-y
> centrally
Hi Mark,
Thanks.
The problem is that only the slab shifts and water molecules stay x-y
centrally in the box. Similar to the picture in the link below:
https://drive.google.com/open?id=1TwkgpesJPfFUiqxhl9rXBU33dwWn-tyD
Regards,
Alex
On Fri, May 25, 2018 at 5:30 AM, Mark Abraham
wrote:
> Hi,
>
> m
Hi,
mdrun suits itself because there's no way to guess how to keep everybody
happy with the form of the output.
You shouldn't need to care, but if you want to put the center of the box
somewhere, editconf and trjconv do that.
Mark
On Thu, May 24, 2018 at 9:58 PM Alex wrote:
> Dear all,
> I ha
Dear all,
I have system containing a solid slab and water molecules on top of it in a
rectangle box ( 6.67350 , 6.96840, 8.68584). I do not know why the whole
slab completely shift in the Y direction after minimization!? The shift
approximately is equal to the Y-cell size (6.96840). It might not
