[gmx-users] gmx distance

Hello Dear All I did a simulation of protein-protein interaction. I want to obtain a distance residue between the two proteins. In the Gromacs tutorial has been said to calculate of distance for protein-ligand whereas I want to calculate of distance for protein-protein. The command of

[gmx-users] Periodic Boundary Conditions

Hello I want to do noPeriodic Boundary Conditions for my system. Gromacs tutorial has said that it can not be used the center and nojump in one command simultaneously. I would be grateful if you could explain the reasons for it? please see this tutorial

[gmx-users] RMSD plots protein-protein complex

Hello I did a simulation of protein-protein interaction with Gromacs code. In this simulation, the number of amino acids in each protein is about 230. The simulation production run was 300ns. After analyzing trajectory, I found that RMSD value of protein-protein complex fluctuated near 1.8 nm but

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