I am performing protein ligand simulations in Gromacs. In md simulations how can one fix these dangling movements of residues near protein terminals? I think this will interfere in my RMSD or RMSF plots. is it possible to fix them in trajectory or some preparatory modification is required?
Rahul Suresh
Hi
This is just PBC error.
gmx trjconv -f md.xtc -s md.tpr -o pbc.xtc -pbc mol -ur compact -center/centre
try this.. -pbc have several other options. kindly go through the manual
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Norman Geist
Rahul Suresh In fact it's not quite an error, just a question of representing a periodic system ;)
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