Re: [gmx-users] Umbrella sampling-protein-ligand complex

2012-09-28 Thread Justin Lemkul
On 9/28/12 2:19 PM, Archana Sonawani wrote: Dear Justin, So do I have to carry out umbrella sampling simulations separately for the three complexes or put the three ligands together with the protein and pull the ligands one by one to calculate the binding energy. I am confused. Each complex

Re: [gmx-users] Umbrella sampling-protein-ligand complex

2012-09-28 Thread Archana Sonawani
Dear Justin, So do I have to carry out umbrella sampling simulations separately for the three complexes or put the three ligands together with the protein and pull the ligands one by one to calculate the binding energy. I am confused. Thanks in advance. Regards, Archana On Fri, Sep 28, 2012 at

Re: [gmx-users] Umbrella sampling-protein-ligand complex

2012-09-28 Thread Justin Lemkul
On 9/28/12 9:27 AM, Archana Sonawani wrote: Hi, I have performed simulations for 3 different ligands complexed with the same protein. I want to compare the binding energies of these different three complexes. Will umbrella sampling be useful in this case? Several methods could be used, and