GROMACS version: Any GROMACS modification: No Is there any way to use pbc for the simulation, but have the output .trr file come with pbc already removed? Or must I complete the whole simulation and then go back and process the data using gmx trjconv? It would be much more convenient for me to be able to simply remove the pbcs in real time as it prints to the .trr. Thank you. …

GROMACS version: version 2021.5 GROMACS modification: Yes/No Here post your question Hello Gromacs users, I’m a beginner computational chemistry student using Gromcs for my undergraduate research. I capped a 3 nm Silver nanoparticle with amino acid ; ARG and carried out umbrella sampling by pulling one amino acid residue away from the nanoparticle. I followed the umbrella sampl…

GROMACS version:version 2021.3-MODIFIED GROMACS modification: Yes Hi, I have a small system with 87 residues of a protein. And I want to maintain the tertiary structure of the protein, so I came up with some restraints which I am supplying in the topology file under the [bonds] directive. It is as follows 137 1188 6 3.253 8000 271 1125 6 3.043 8000 …

Dear all, I would like to calculate the glass transition temperature of a polymer in Gromacs. What is the best way to calculate it? I know there is no direct way. However, I have no idea how to calculate it. Thanks a lot 1 post - 1 participant Read full topic