GROMACS version: GROMACS modification: No @jalemkul HI Everyone, Is there any certain number of minimum steps defined to run the equilibration (NVT and NPT)? i.e we are free to choose the number but curious to know the minimum steps required to equilibrate. How to decide the number of nsteps? Thanks 1 post - 1 participant Read full topic

GROMACS version: 5.1.4 GROMACS modification: No Respected community members, I have one basic doubt regarding the frames in trajectory. I have done a 100 ns simulation and while doing analysis such as rmsd, distance estimation, and end frame extraction I am getting confused with the output printed on the terminal. While performing distance analysis using gmx distance command, th…

GROMACS version: GROMACS modification: Yes/No Here post your question I have been trying to add NAG to forcefield Gromos54a7: Fatal error: Residue ‘NAG’ not found in residue topology database I have generated a forcefield.itp and topology for NAG through CHARMM-GUI. I have added NAG to the aminoacids.itp I have #include “toppar/forcefield.itp” in the Gromos54a7 forcefield.i…