[gmx-users] Drug moves out of the nanocarrier

faride badalkhani farideh.khamseh at gmail.com
Thu Apr 20 08:24:56 CEST 2017

Dear Gromacs users,
I am trying to perform PMF calculations on a nanocarrier-drug system. The
procedure I have performed is as follows:
1) running MD simulation on the unloaded nanocarriers for 30 ns
2) insertion of drug into nanostructure using AutoDock
3) running production MD simulation on the nanocarrier-drug for more 30 ns
4) umbrella sampling and PMF calculations

I have completed this procedure for 5 systems, but for the last one drug
moves out of the nanocarrier after 5 ns, and I do not know how to sole the

Any comment or suggestion will be greatly appreciated.


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