GROMACS version: 2018.1
GROMACS modification: Yes/No
Here post your question
Q. How to select frames or conformations for umbrella samplig?
I have run umbrella sampling after steered MD simulation for RNA system by taking equidistant of 0.2 nm between two consecutive .gro files for 5 windows and did WHAM analysis for same but I didn’t get overlapped histogram. I have also tried with different time steps as well different distance spacing but I’m facing same problem with them also. I can provide files (summary_distance.dat, profile.xvg, histo.xvg and .gro files) if required.
I have used the following command for WHAM analysis:
gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal
Query: So my question is- how can we get overlapped histogram from umbrella sampling and what is the basis of selecting the conformation for umbrella sampling for to get overlapped histogram.
Thanks and Regards…