[gmx-users] umbrella sampling-Bimodal Histograms
ammasachu at gmail.com
Tue Jun 22 05:08:21 CEST 2010
I am doing US . Yes, histograms of population densities along the reaction
coordinate. Please find the pull settings. Sampled for 800ps.(nsteps =
400000). Pull_init will vary for each frame, depends on the window spacing.
pull = umbrella
pull_geometry = position
pull_dim = N N Y
pull_start = no
pull_nstxout = 10
pull_nstfout = 10
pull_ngroups = 1
pull_group0 = U_ref
pull_pbcatom0 = 0
pull_group1 = r_C1
pull_pbcatom1 = 0
pull_init1 = 0 0 0.1
pull_k1 = 1000
pull_rate1 = 0
pull_vec1 = 0 0 0
Please check this link for my histograms
I would greatly appreciate our suggestions.
On Mon, Jun 21, 2010 at 8:14 PM, <chris.neale at utoronto.ca> wrote:
> Please clarify:
> Are doing SMD or are you doing US? If you're doing SMD then you should not
> be using WHAM and you should not really be able to generate any sampling
> Are the histograms that you are referring to population densities of the
> sampling along your reaction coordinate?
> My guess -- if you're doing US -- is that you have some incorrect pull
> group settings. Bimodal distributions are indeed possible, but should
> require very long sampling times to achieve, and I doubt that you are at
> those times yet. Your Fc is fine. Post your pull settings.
> -- original message --
> When i did the Umbrella sampling of frames from an SMD (of ligand
> transport), I am getting bimodal histograms in some cases.
> Do you think this is because , the force constant that i used is very low
> used pull_k1=1000).? Are these bimodal peaks may cause any deviation in my
> PMF result? Do I need to repeat the sampling again with another pull_k1
> value(higher value)?
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