Re: [gmx-users] REMD Plots

Hi Shan, I am not quite sure if you want to generate an REMD simulation mobility in temperature space for the 30 replicas. If that be the case, then you can use the data in the replica_temperature.xvg file to plot replica index vs REMD steps. The 1st column in the file corresponds to the REMD

[gmx-users] An atom is beyond the wall in gromacs2018

Hi Gromacs Users I did a simulated annealing MD with gromacs/5.0.1 and gromacs/2018. In both cases I had the same input configuration and parameters for the potential wall. The simulation with gromacs/5.0.1 did achieve convergence but with the gromacs/2018, an atom always go beyond the wall. Can

[gmx-users] An atom is beyond the wall in gromacs2018

Hi Gromacs Users I did a simulated annealing MD with gromacs/5.0.1 and gromacs/2018. In both cases I had the same input configuration and parameters for the potential wall. The simulation with gromacs/5.0.1 did achieve convergence but with the gromacs/2018, an atom always go beyond the wall. Can

[gmx-users] Module for spectroscopy analysis

Hi gromacs user, I want to perform a spectroscopic analysis of amino acids. Is there any module in gromacs to help me with that. Kind regards Joel -- Joel Baffour Awuah PhD Candidate *Institute for Frontier Materials* *Deakin University* *Waurn Ponds, 3126 VIC* *Australia +61450070635