GROMACS version: 2020.5
GROMACS modification: No
Hello everyone! I have the eingenvectors for my protein structures ensemble through gmx colvar using the backbone coordinates for the calculation. Analysing the projections on PC1 and PC2 it was possible to identify two states in the system. I then generated a possible transition path selecting two representative configurations between the two states and making a linear interpolation between then in cartesian space, carefully minimizing the side chain conformation in each step so that I could get good structures. I was now wondering if I could possibly run an umberlla sampling simulation with the points I’ve generated, maybe using gmx mdrun with the sam.edi input file generated by gmx make_edi. Reading the documentation I’ve found out that specifying the -flood option together with the -restrain option, gromacs would keep the pc1 value restrained during the simulation in each window. But I don’t know if I can somehow use gmx wham with the information outputted in edsam.xvg. I hope my question was clear, thanks for the attention!
So I finally found how to do it. The command line for generating sam.edi should be something like:
gmx make_edi -f eigenvec.trr -eig eigenval.xvg -s topol.tpr -flood 1 -harmonic -restraint -tau 0 -Eflnull -10000
Specifying tau = 0 means that the flooding will be constant, that is, the force constant of the harmonic potential will not change during the simulation. Eflnull will specify the magnitude of the force constant, so if the eigenvalue of the eigenvector you are trying to restrain is 50, than the force constant will be (1/50)*Eflnull. To analyze the results you can use the WHAM package, once the gmx wham tool seem to work only with the results of pull setups.