I have made an MDS using NAMD for a protein-ligand complex with periodic boundary conditions (PBC) and I want to analyze the data.
what are the steps that I should follow to prepare my system for analysis?
for example, removing the PBC, aligning frames. And what are the commands I should use in VMD to do the preparation?
thanks
Aligning is useful for visualization (no drift) and necessary for measuring distances between atoms from different frames (e.g., RMSD). No pre-processing is necessary for analyses that do not directly compare different frames (e.g., secondary structure assignment, hydrogen-bonding interactions).
Martin Klvana Thanks for your answer sir
if my system is broken due to PBC, should I remove the PBC, and how to remove it in vmd?
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