Dear GMX users, I'd like to perform the umbrella sampling using the pull codes in gromacs. The reaction coordinate is defined as the distance between the center of mass (DCOM) of two domains in a protein. The following script is used: ------------------- only for pull section ; Pull code pull = umbrella pull_geometry = distance pull_dim = N N Y pull_start = no pull_ngroups = 1 pull_group0 = NN1 ; contained in index file pull_group1 = NN2 ; contained in index file pull_init1 = 2.5 pull_rate1 = 0.0 pull_k1 = 20000 ; kJ mol^-1 nm^-2 pull_nstxout = 5000 ; every 2 ps pull_nstfout = 5000 ; every 2 ps -----------------
I have two questions about the output of gromacs: 1. How is the energy term "COM Pull En." in *.log file calculated? Is it computed as 1/2*kf*(DCOM_t - pull_init1)^2 at time t? 2. Where is the output information for the evolution of DCOM? Is it in the file pullx.xvg? Many thanks. Mingjun -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
