[gmx-users] Umbrella Sampling - Justin tutorial

Hi GMX Users, I am doing Justin tutorial of Umbrella sampling. I have just finished continous pulling of chainA from the reference chainB. I have some questions. I looked at the trajectory of pulling and it has began with dissociating residue 27Alanine from the ChainB following 26, 25, 24...1. My

Re: [gmx-users] Umbrella Sampling - Justin tutorial

Steven Neumann wrote: Hi GMX Users, I am doing Justin tutorial of Umbrella sampling. I have just finished continous pulling of chainA from the reference chainB. I have some questions. I looked at the trajectory of pulling and it has began with dissociating residue 27Alanine from the

Re: [gmx-users] Umbrella Sampling - Justin tutorial

Thank you Justin, now I get what you mean! As I understood I should pick just one frame untill 189 ps (when dissociation occured) - does it matter which one I will choose on the final binding free energy? Then spacing should be 0.2 nm. Right? But how is it possible to do spacing like this from

Re: [gmx-users] Umbrella Sampling - Justin tutorial

Steven Neumann wrote: Thank you Justin, now I get what you mean! As I understood I should pick just one frame untill 189 ps (when dissociation occured) - does it matter which one I will choose on the final binding free energy? The free energy minimum should (theoretically) be when the

Re: [gmx-users] Umbrella Sampling - Justin tutorial

Thank you Justin! That helped a lot! Steven On Wed, Nov 16, 2011 at 3:06 PM, Justin A. Lemkul jalem...@vt.edu wrote: Steven Neumann wrote: Thank you Justin, now I get what you mean! As I understood I should pick just one frame untill 189 ps (when dissociation occured) - does it matter