[gmx-users] PBC fix for visualization

[Mohsen Ramezanpour]

Hi Dallas,

Thanks for your reply.
I did try -pbc cluster for waters. It could fix it somehow but not
completely.
After that, I had to use -pbc center to fix it. Still, I do not get what I
want.
Unfortunately, some waters and lipids are appearing from the other side of
the box.

Cheers,
Mohsen


On Sun, May 21, 2017 at 8:12 PM, Dallas Warren <dallas.warren at monash.edu>
wrote:

> I have found the cluster option of -pbc to work well for putting
> aggregates back together correctly. Some times you do need an index
> file and appropriate groups to assist with it getting it right.
>
> gmx trjconv -pbc cluster
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.warren at monash.edu
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
> On 16 May 2017 at 07:50, Mohsen Ramezanpour
> <ramezanpour.mohsen at gmail.com> wrote:
> > Dear Gromacs users,
> >
> > I have an HII phase made of one inverted cylinder (and waters inside) in
> a
> > triclinic box with 90, 90, 60 angles. After running the simulation, this
> > cylinder become bent like a curve. I.e. is not a perfect cylinder
> anymore.
> > As a result, some water molecules and lipids pass the box sides and enter
> > from the other side of box because of PBC.
> > Now, I want to make the cylinder again but I am not sure how to do so.
> >
> > The best I could do was to use "-pbc mol  -ur compact" options in
> trjconv.
> > However, here are still some lipids and molecules which are not part of
> the
> > cylinder.
> >
> > Any idea how could I fix the effect of these PBC in visualization?
> >
> > Thanks
> > Mohsen
> >
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-- 
*Rewards work better than punishment ...*