[gmx-users] ligand is out side the box

[Tsjerk Wassenaar]

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Cheers,

Tsjerk


On Fri, Aug 22, 2014 at 11:37 AM, RINU KHATTRI <nickname.mittu at gmail.com>
wrote:

> hello gromacs users
> i am working on protein ligand complex with POPC membrane according to
> justin (from previous mail) i built the system without ligand and
> after minimization and shrink paste the ligand and edit the box size
> but after solvation and water addition ligand is out side the box
>
> grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr
>
> genion -s ions.tpr -o system_solv_ions.gro -p topol.top -pname NA
> -nname CL -nn 14
>
> grompp -f minim.mdp -c system_solv_ions.gro -p topol.top -o em.tpr
>
> gmx mdrun -v -deffnm em
>
> you can see the image i have been uploaded
> kindly help
>
> http://s48.photobucket.com/user/mittukhattri/media/pic_zpse022cdb3.png.html?filters[user]=140927090&filters[recent]=1&sort=1&o=0
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-- 
Tsjerk A. Wassenaar, Ph.D.