GROMACS version: GROMACS modification: No Hi @jalemkul I have run the MD simulation (protein-lignad) by following your protocol (http://www.mdtutorials.com/gmx/complex/index.htm). Also at the end of simulation, I recentered and rewrapped the coordinates using gmx trjconv command. In MD simulation movie it gives weird outcome. I ran MD simulation for 200 ns. Energy minimization…

Is there any way by which we can write gromacs calculated energies in a separate data file (such as <.txt> file) during MD run? I know (1) we can extract the energies from <.edr> file. (2) even we can use gmx dump to see/read the contents of <.edr> file. (3) The same energies are also written in log file But in all the three cases, the precision is poor. I …

Hello Everyone, I am trying to form a water droplet on graphene sheet, to calculate its contact angle for better understanding. But, the droplet is moving all around the sheet. Can anyone tell me how to fix the center of mass of the droplet or how to get a droplet so that it can retain in one place? 20nm x 20nm graphene sheet with 3000 water molecules. any command that can fix c…

I’m trying to make an analysis package of mine compatible with triclinic cells, particularly with Gromacs dodecahedal and octahedral cells. Yet, I’m not a regular Gromacs user and I struggling to obtain something that is probably very simple (so simple that tutorials do not follow that route). What I want to obtain is a box of ~10k Neon atoms (available at the OPLS force field), …

GROMACS version: GROMACS modification: Yes/No Here post your question Hello! I am currently using gRINN software to conduct energy scoring analysis on my simulation data. I input three files from the simulation into gRINN: TOP, TPR, and XTC. I had modified each of the files to remove the water and ions, just leaving the proteins, as is recommended by gRINN. Both the Filtering a…