Dear Plumed users,
Currently, I am in the process of bias-exchange metadynamics and analysis.
I have successfully executed the simulations using the However, due to a lack of background knowledge, I am encountering challenges in conducting a comprehensive analysis.
During my search for solutions, I came across the article 'Analyzing and biasing simulations with PLUMED,' (
https://arxiv.org/pdf/1812.08213.pdf) which seems promising.I intend to follow the guidelines outlined in this article. Specifically, I plan to use PLUMED's
WHAM_HISTOGRAM tool for my analysis.
The command lines that I used are summarized below
1. plumed-common-1.dat file contains and defines 8 CVs.
2. mpiexec -np 8 gmx_mpi mdrun -plumed plumed.dat -v -deffnm production -multidir be0 be1 be2 be3 be4 be5 be6 be7 -replex 1000
3. plumed_what.dat file as input for plumed WHAM_HISTOGRAM as below
- INCLUDE FILE=plumed-common-1.dat
h: WHAM_HISTOGRAM ...
ARG=interact,alpha BIAS=*.bias TEMP=300
GRID_MIN=0,0 GRID_MAX=400,8.0 GRID_BIN=200,16
BANDWIDTH=0.1,0.1
fes: CONVERT_TO_FES TEMP=300 GRID=h
DUMPGRID GRID=fes FILE=fes.dat
However, I am uncertain about the exact procedure for utilizing
WHAM_HISTOGRAM effectively. If anyone has experience or insights into this, I would greatly appreciate your guidance.
My question is that
1. how does the
WHAM_HISTOGRAM work?
2. while I have obtained output files, I am unfamiliar with their format and struggle with interpreting them. Could anyone provide guidance on how to read and interpret theses output files?
Thank you. I look forward to your valuable insights.
Best regards,
Jinyoung