Re: [gmx-users] Number of windows in umbrella sampling

Justin A. Lemkul wrote: shahid nayeem wrote: Thanks Justin. I will try again. But please refer to some protocol if you know and one last question that before doing umbrella sampling simulation how can one be sure that the pulling is good and one should go ahead with selecting window and do

Re: [gmx-users] Number of windows in umbrella sampling

shahid nayeem wrote: Thanks Justin. I will try again. But please refer to some protocol if you know and one last question that before doing umbrella sampling simulation how can one be sure that the pulling is good and one should go ahead with selecting window and doing umbrella sampling. In t

Re: [gmx-users] Number of windows in umbrella sampling

Thanks Justin. I will try again. But please refer to some protocol if you know and one last question that before doing umbrella sampling simulation how can one be sure that the pulling is good and one should go ahead with selecting window and doing umbrella sampling. In the end when you see histo.x

Re: [gmx-users] Number of windows in umbrella sampling

shahid nayeem wrote: Thanks for quick reply. I have created mutant of a complex by changing interface residue in VMD. These mutant are experimentally known to show less binding affinity. I want to reproduce these results with umbrella sampling. Now I am sending profile and histo file for wt a

Re: [gmx-users] Number of windows in umbrella sampling

shahid nayeem wrote: Dear Justin I am doing umbrella pulling simulation of a protein complex wt and mutant. I expect mutant to give lower deltG value. I am attaching a tif file of energy vs time curve of wt and mutant protein on pulling simulation. These energies are obtained by g_energy and