[gmx-users] Periodic boundary conditions during the simulation

[Dallas Warren]

Boundaries of the box used for visualisation are totally arbitrary, it
makes not difference when the various simulations are being performed.
Most efficient to simply process it at the end to get the visual
representation you want

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 Fri, 24 Apr 2020 at 12:29, Mohamed Abdelaal <m.b.abdelaal at gmail.com>
wrote:

> Hello everybody,
>
> I know that due to periodic boundary conditions the molecules move from one
> side of the box to the other side and moves outside the box. I also know
> how to use trjconv to solve this problem and I usually do this step at the
> end of the simulation. However I have noticed that after the energy
> minimization, some molecules which were position restrained at the bottom
> of the box have been moved to the top of the box. I knew that I have this
> periodic boundary condition problem not just from visualization of the
> structure after the energy minimization, but also from the atoms
> coordinates in the .gro file after the energy minimization, the z
> coordinate of some atoms have been changed from bottom to top as below:
>
> before energy minimization: (the z coordinate was always zero)
>
>     1GRM     C1    1   0.061   0.071   0.000
>     1GRM     C2    2   0.184   0.142   0.000
>     1GRM     C3    3   0.184   0.284   0.000
>     1GRM     C4    4   0.061   0.355   0.000
>     2GRM     C1    5   0.061   0.497   0.000
>
>
> after energy minimization: (z coordinate of some atoms have been changed
> into 14 which is at the top of the box)
>
>     1GRM     C1    1   0.061   0.071  14.000
>     1GRM     C2    2   0.184   0.142  14.000
>     1GRM     C3    3   0.184   0.284   0.000
>     1GRM     C4    4   0.061   0.355   0.000
>     2GRM     C1    5   0.061   0.497  14.000
>
>
>
> Do I need to solve this PBC problem between the different steps (energy
> min, NVT, NPT, production run) or it is okay to continue my simulation
> (even if the molecules have moved) and solve this problem at the end ?
>
> Many thanks,
> Mohamed
> --
> 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.
>