Umbrella sampling output

User discussions
1

GROMACS version:2019.2
GROMACS modification: Yes/No
After performing umbrella sampling on wild-type Aβ42 protofibril , I have obtained a graph for PMF. It has many fluctuations when i compare it to the graph in the tutorial. This is the image of my PMF graph
photo
X AXIS: REACTION COORDINATE, Y AXIS: PMF

P.S: Post running the command gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal
I got many warnings like no data-point in bin 162(z = 3.16453) you may not get a reasonable profile check your histogram!

2

This means you probably did not choose very good initial configurations as the basis for your windows, leaving gaps in the sampling along the reaction coordinate.