[gmx-users] PBC fix for visualization

Dallas Warren dallas.warren at monash.edu
Mon May 22 04:13:20 CEST 2017


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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