[gmx-users] mirror effect in membrane simulation

[manindersingh rajawat]

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