From: zeynab hosseini (
Date: Wed Apr 15 2020 - 00:08:45 CDT

Dear All,

I'm new in the umbrella sampling (US) method. I followed the NAMD tutorial
performing US technique to calculate the adsorption free energy of an amino
acid (AA) on (infinite) single-walled carbon nanotube (SWCNT) surface. I
used the weighted histogram analysis method (WHAM) to reconstruct the
potential of mean force (PMF) from biased potential. The point is that we
expect the pmf flatten when the AA distance from the CNT increases. But, as
it is seen in the attached plot, the pmf reduces when the AA is getting
close to the simulation box edges (around 30A). I wonder why this reduction
happens. I reviewed namd-l following all related suggestions. Moreover, Iā€Œ
plotted pmf every 6ns and Iā€Œ need help to conclude whether the pmf is
converging. The windows overlap is good... I also attached the colvars
input file ( and configuration file (win-base.conf)ā€Œ if it is
conjectured something is wrong with them...

The CNT is fixed at the center of the 60A *60A *30A simulation box of water
molecules and oriented along the z-axis. The reaction coordinate is the
radial distance of the AA from the center of the CNT. The bounds of the
reaction coordinate are 6.8A and 27.8A and the windows are spaced 1A apart,
centered at 6.8A, 7.8A...27.8A. Each window is sampled for 38ns. The force
constant is 2.5kcal/mol.

Would be thankful if anybody guides me.
All the best,

** Visit for more info on majordomo