[gmx-users] helping increasing box

[Alessandra Villa]

Hi,

What you see, is the effect of boundary condition.To avoid this
visualization effect,
before increasing the box, you may want to check that your system is whole
and better center in the gro file.

Best regards
Alessandra



.
On Thu, Nov 14, 2019 at 10:28 PM Giuseppe R Del Sorbo <del-sorbo at ill.fr>
wrote:

> Dear all,
>
> I am doing COM-pulling simulations between two lysine chains connected
> with a surfactant.
>
> Basically I want to find the force able to separate the two chains.
>
> Increasing the force, at some point gromacs was complaining that the
> distance between the two pull groups is larger that the half of the box
> lenght.
>
> To solve this problem, I increased the box size but now the two lysine
> are not
> connected anymore.
>
> When I open with vmd the .gro file, the two chains are not connected but
> far away because, of course, I increased the box.
>
> I should move the two chains at the end of the box. In this way when on
> VMD I add other boxes in +y and -y directions I will able to see the two
> chains connected and not separated from a gap dipending on the
> increasing of the box.
>
> But I don't know how to do this.
>
> Do you have any suggestion?
>
> Thanks
>
> Giuseppe
>
>
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>