GROMACS version: 2021
GROMACS modification: Yes/No
I performed an umbrella sampling using as CV the rotation angle of protein helix. But I didn’t use pulling md to produce configurations. I used enforced rotation to generate the configurations. And my question is: if can I use WHAM analysis tool with the output files generated from enforced rotation as input files?
Note: To perform umbrella sampling I based on gromacs tutorial of umbrella sampling and performed at each configuration the enforced rotation with 200kj/mol of applied force and 0 degrees/ps of angle rate. So the helix will not rotate at the simulations.
No, I didn’t receive any answer, but I tried use Alan Grossfield’s WHAM software but I failed because the files with the rotation angle have only zeros. I don’t know if this were possible to do. Now, I’ m trying with an alternative CV with metadynamics with plumed. Here, I left the link. https://groups.google.com/g/plumed-users/c/JoV6hZrFTwk/m/IVSEh0K1BwAJ
Hi, i tried enforced rotation with rot-fit-method0 = rmsd ; (rmsd, norm, or potential).
It does not give rotation angle as 0 in output files but fluctuating about 0 (method=potential gives all zeros). So, I’m currently trying umbrella sampling with rot-fit-method0 = rmsd and then will use Alan Grossfield’s WHAM to get PMF. I’ll let you know if it works.
Hi, I had been using rmsd fit method, but in somes simulations at rotation angle of 100º or upper, I had only zeros in rotation angles and in column fit-angle values with variation of 180º. My idea was if the variation of fit-angle were around zero, I could sum the inital rotation angle (10º, … , 90, … , 180º ) to create the histograms and then calculate WHAM with Alan Grossfield softwhare, but I couldn’t. But after you wrote me these, I tried to use potential fit method and I had only zeros in rotation angle column and values around zero in the fit-angle column. And now, I could sum the initial rotation angle and got the histograms. Thanks to your help I could do this when I’ ve given up with to do umbrella sampling using enforced rotation and I was abandoning one of my PhD thesis objetives. I hope this could help you with your work.