[obasekia]

I have followed the tutorial for the GaMD simulation for alanine dipetide and i would like to ask if i wanted to calculate the Free energy landscape (FEL) of other parameters like radius of gyration and RMSD what selection key words can i use for my CV.dat file

[oshima]

Hello obasekia,

In the GaMD tutorial, the FEL is calculated by employing the diheral angles as the CVs and the diheral angles are calculated using “trj_analysis”. If you want to use the Rg or RMSD as the CV, you should calculate it using “rg_analysis” or “rmsd_analysis”, respectively. Usage of the analysis tool is explained in “Samples2021” of this web site ( https://www.r-ccs.riken.jp/labs/cbrt/samples2021/ ). Please see the page. By saving the trajectory data of Rg or RMSD to “cv.dat” and following the same reweighting procedure in the tutorial, you can obtain the FEP of interest.

Thank you,

Hiraku Oshima