[gmx-users] mirror effect in membrane simulation

Dallas Warren dallas.warren at monash.edu
Tue Oct 16 00:27:29 CEST 2018

Nothing being done wrong at all, it's a visualisation artefact.
Performing the Hbond calculations on the unprocessed trajectory will
not affect the results, the various scripts involved in such analysis
are intelligent enough to handle the PBC.

The command you invoked there does nothing to center the bilayer in the box.
# mol puts the center of mass of molecules in the box
# compact puts all atoms at the closest distance from the center of the box.

See http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
for pointers.

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 Mon, 15 Oct 2018 at 17:58, manindersingh rajawat
<rajawat.manindersingh at gmail.com> wrote:
> Dear gromacs users,
> I performed 200ns MD simulations (gromacs 5.0.7) of peptide and lipid
> bilayer. Placed 6 copies of the peptide(12 aminoacids long) over the
> surface of the lipid bilayer(128 lipids, 64 in each leaflet). Upon
> visualizing the trajectory, observed that few copies of the peptides cross
> the bilayer during simulation. I think its due to mirror effect. As I want
> to calculate hydrogen bond occupancy between peptide and lipids over the
> simulation time and distance between center of mass of peptide and lipid
> molecule. How it affect these calculations? How to remove this effect?  and
> where I am doing wrong.
> I run the command but no success: gmx trjconv -f pre.xtc -s pre.tpr -o
> new.xtc -b 0 -e 200000 -ur compact -pbc mol
> Please advise with appropriate commands.
> Thanks and regards,
> Maninder
> --
> Maninder Singh
> Research Fellow,
> LSN-104, Computational Biology and Bioinformatics Unit,
> Molecular and Structural Biology Division,
> CSIR-Central Drug Research Institute,
> Sector-10, Janakipuram Extension,
> Sitapur road,
> Lucknow
> India-226031
> M: +919129206276
> Email: rajawat.manindersingh at gmail.com
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