[gmx-users] query regarding coming out of ligand from protein during simulation

[sangeeta kundu]

Dear all,
 
 
 
    I am trying to perform simulation of a protein with several ligands, in case of certain ligands I found that the ligand  is coming out of the protein after 5-6 ns. I have checked the energy of the system, but it does not show any abrupt change, still the ligand is coming out of protein after a certain time.Is it due to steric hindrance during the course of the simulation or something else?   I can not debug, please help. Thanks in advance. 
 
 
regards
Sangeeta


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