[gmx-users] Correcting PBC effects

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Feb 21 11:04:24 CET 2012

Hi Ariel,

If it works, it's good :)
It really only affects the visualization... It doesn't change the system.



On Tue, Feb 21, 2012 at 10:33 AM, Siew Wen Leong
<ariel.leongsw at gmail.com> wrote:
> Dear all,
> Have anyone tried using CHARMM36 equilibrated POPE bilayer by Dr.Klauda
> http://terpconnect.umd.edu/~jbklauda/research/download.html?
> I am planning to use the membrane patch for a transmembrane protein
> simulation. At first visualization, the membrane patch consists of a bilayer
> with a single layer of water and then several lipids sticking out from the
> opposite side of the water. So I presumed that to be an effect of PBC.
> How can I correct this in Gromacs?
> I've generated a .tpr for the system to use trjconv to manipulate the PBC
> box.
> Out of all the combinations of pbc treatments, this one works:
> trjconv -f pope80-c36box.gro -o pope80_pbc10.gro -s pope80.tpr -pbc mol
> This puts the center of mass of the molecules in the box so I got a lipid
> bilayer with a single, thick layer of water.
> then followed by
> trjconv -f pope80_pbc10.gro -o pope80_pbc11.gro -s pope80.tpr -pbc mol
> -center
> to center the membrane on POPE.
> The result looks fine (a hydrated bilayer) but I'm a new user to Gromacs so
> I just wanted to ask if the workflow is reasonable.
> --
> Regards,
> Ariel.
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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