GROMACS version: 2018.4 GROMACS modification: Yes/No In the process of MD simulation, the first step of converting pdb to gmx ask to select the type of N terminal and C terminal of the amino acids. The options are as NH3+, NH2 and COO- and COOH for the N terminal and C terminal respectively. Is there a specific reason to select the terminals as NH3+ and COO- and does it change wi…

I am working on MD simulation using gromacs for solid state electrolytes for polymer and run successfully all the simulations. Also did some fine analysis like RDFs calculations for Li and TFSI ions. All results go comparable to literature. But the problem is when calculating MSDs and Diffusion coefficients for Li and TFSI ions. The trends are same but the values which i calculate …

Hello gromacs users, For a peptide structure generated by simulations on gromacs; I see no hydrogen bond occupancy (0%) between two sites 1 and 2 when I apply gmx hbond analysis on this one structure. Attempted default cutoff and higher values. However, when I load the molecule on Pymol, I clearly see a H-bond between those two sites with cut off distance of 2.7 A. I do not under…