Re: [gmx-users] Is minimization and equilibration needed for umbrella sampling?

On 1/13/20 9:22 AM, Qing Lv wrote: Thank you, Justin. I start each run by randomly generate velocities at 300K, and each run is quite stable. So, is it appropriate to regard the first 20 ps (this is a QM/MM MD) of each run as the equilibration and just discard this 20 ps in the final wham a

Re: [gmx-users] Is minimization and equilibration needed for umbrella sampling?

Thank you, Justin. I start each run by randomly generate velocities at 300K, and each run is quite stable. So, is it appropriate to regard the first 20 ps (this is a QM/MM MD) of each run as the equilibration and just discard this 20 ps in the final wham analysis? Best, Qing At 2020-01-13 2

Re: [gmx-users] Is minimization and equilibration needed for umbrella sampling?

On 1/10/20 11:02 AM, Qing Lv wrote: Dear Colleagues, I am doing a QM/MM umbrella sampling to calculate the PMF of an enzymatic reaction. The initial coordinates (with solvents and ions) for each sampling window were extracted from previous trajectories. The reaction coordinate (bond lengt

[gmx-users] Is minimization and equilibration needed for umbrella sampling?

Dear Colleagues, I am doing a QM/MM umbrella sampling to calculate the PMF of an enzymatic reaction. The initial coordinates (with solvents and ions) for each sampling window were extracted from previous trajectories. The reaction coordinate (bond length difference) of each initial frame was c