[gmx-users] protein -ligand complex dissociating during simulation

Sneha Vishwanath snehavishwanath09 at gmail.com
Fri Jul 21 14:56:32 CEST 2017

Dear all

I am simulating a dimeric protein, with each subunit bound to a small
molecule. During the simulation, one of the ligands is dissociating from
the chain and moving all around the chain while the same ligand remains
bound to the chain during simulation. Experiments show that the ligand
binds to both the subunit which is further supported by the experimental
structure of the protein-ligand complex (which I have used for the
simulation). The simulation is for 50 ns and it usually starts dissociating
after 10 ns.

Any thoughts on why could it be happening and how it can be circumvented?
Any help would be useful.

Thanks in advance.

Sneha Vishwanath

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