[gmx-users] Umbrella Sampling and Histogram

[Agnivo Gosai]

Dear Users

I am sharing my umbrella sampling results in line with my previous posts
and queries.

So, here are my data :

This is the Bootstrap profiles plot. I use -nBootstrap = 100 and -bins =
100​
 bsProf.png
<https://docs.google.com/file/d/0B-U8uULVZjfRVnY2QURLeUI2WGc/edit?usp=drive_web>
​
>From the xvg file I found the standard deviation to hover around 1.0
kcal/mol​
 bsResult.png
<https://docs.google.com/file/d/0B-U8uULVZjfRb0t5N1Joc3hjQVk/edit?usp=drive_web>
​
This is the PMF generated over 43 windows of 0.1 nm spacing.​
 PMF.png
<https://docs.google.com/file/d/0B-U8uULVZjfRbDRsLUh5VEdRNlE/edit?usp=drive_web>
​
The histogram distribution looks bad to me. I need to modify window spacing
for a proper overlap.​
 HISTOG.png
<https://docs.google.com/file/d/0B-U8uULVZjfRRGhnOG5qUGhoOVE/edit?usp=drive_web>
​
>From the g_wham paper by Jochen Hub et.al I think the PMF converged from
the standpoint of error analysis.

What are your opinions ?

Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.