Re: [gmx-users] part of ligand molecule leaves protein

Dear Andrew: You can look at temporal profile of area buried at the protein-ligand interface / protein-ligand coordination number. If there is a sharp change at the beginning of simulation it might be indicative of improper equilibration of complex. A gradual change over initial few nanoseconds

[gmx-users] part of ligand molecule leaves protein

Hi gromacs users, I did md simulation of the protein-ligand complex. As shown in figure, after 50 ns, part of ligand molecule leaves protein. I remind that I resolve pbc problem at first. https://1drv.ms/u/s!AveJH4Y30cH0tFp_XYCqkrCd7Kqq What is the reason of this state? Best, Andrew --