Dear all,
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.
I think you can check periodic image using VMD and try to use nojump option instead of -pbc mol option.
Thank you
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