Re: [gmx-users] Re: umbrella sampling with "pull=constraint"

From: "Justin A. Lemkul" mailto:jalem...@vt.edu>> Subject: Re: [gmx-users] Re: umbrella sampling with "pull=constraint" To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>> Message-ID: <4eb7f727.3000...@vt.edu <mailto:4eb7f727.3000...

[gmx-users] Re: umbrella sampling with "pull=constraint"

sampling windows? this observation is from last 10ns of 20ns simulation. > > Message: 3 > Date: Mon, 07 Nov 2011 10:20:07 -0500 > From: "Justin A. Lemkul" > Subject: Re: [gmx-users] Re: umbrella sampling with "pull=constraint" > To: Discussion list for GROMA

Re: [gmx-users] Re: umbrella sampling with "pull=constraint"

Vijayaraj wrote: and also I tried to plot the PMF curve from this data, I got few warning messages like "no data point in bin 20, You may not get a reasonable profile. Check your histograms!". the histogram shows poor sampling from 0.6 nm to 0.7 nm, and the windows in this position completely

[gmx-users] Re: umbrella sampling with "pull=constraint"

and also I tried to plot the PMF curve from this data, I got few warning messages like "no data point in bin 20, You may not get a reasonable profile. Check your histograms!". the histogram shows poor sampling from 0.6 nm to 0.7 nm, and the windows in this position completely overlaps at 0.5-0.6 nm

[gmx-users] Re: umbrella sampling with "pull=constraint"

Hello, Thanks for the suggestions. I did umbrella simulation for 20ns and the pull force is as below. 19960.-6.78192 19962.33.3579 19964.-3.1808 19966.-15.0304 19968.-55.4436 19970.-38.9422 19972.-9.41927 19974.-5.95981 19976.