[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
> --
> *Rewards work better than punishment ...*
> --
> 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.

More information about the gromacs.org_gmx-users mailing list