[gmx-users] Regarding high RMSD

[Ashma Khan]

Thank for your suggestion Alessandra
I have applied the pbc conditions on my system in steps as follows:
1. gmx trjconv -f full_md.xtc -s full_md.tpr -pbc whole -o full_md_whole.xtc
2. gmx trjconv -f full_md_whole.xtc -s first_frame.gro -pbc nojump -o
full_md_nojump.xtc
3. gmx trjconv -f full_md_nojump.xtc -s full_md.tpr -pbc mol -ur compact
-center -o full_md_mol.xtc
After applying all these conditions, peptides of dimer diffusing out of the
box, both in opposite direction at the end of the simulation. kindly
suggest me what should I do.

-- 
Ashma Khan
Research Scholar
Department of Chemistry
AMU, Aligarh