Importance of RMSD in GROMACS
I have a trajectory file of about 1000 frames which I have calculated a center of mass for each frame. I would like to use the first frame as a reference and see how much the center of mass...
04 February 2021 5,774 1 View
I need to estimate the mobility of some atoms in the molecule within a molecular dynamics simulation and compare the values for different simulations. I use trjconv -fit rot+trans to fit C-alpha...
19 January 2021 531 3 View
I have been processing some trajectory files from my molecular dynamics simulation using GROMACS by removing pbc, which often requires a sequence of gmx trjconv steps. This time, my protein...
30 December 2020 849 4 View
I'm currently running a protein simulation on GROMACS. I was originally using CHARMM22/CMAP for the simulation, but with some reasons I decided to switch to CHARMM36. The thing is, I expected...
10 November 2020 8,906 1 View
Recently, I have been dealing with symmetrical docking of protein complexes and I have a problem. Well, I have no problems with docking complexes with cyclic symmetry, it is double-walled symmetry...
09 May 2020 4,424 3 View
Hello brilliant researchers! After virtual screening, I performed MD Simulation via GROMACS to check the stability of the protein-top hit complex by following this tutorial...
26 December 2019 2,228 8 View
I need to measure the aggregation of a type of molecule. The aggregation will happen if the COM of molecules becomes less than 0.85 nm. I think I should use g_clustsize but it normally calculates...
11 December 2019 2,207 4 View
11 December 2019 5,952 4 View
Dear researchers I have performerd a protein ligand interaction using gromacs but I am unable to do the RMSD and other analysis of the protein+ligand complex for comparing it with only the Protein.
10 November 2019 7,161 5 View
I was run 100ns MD simulation for native and mutant structures. Although, RMSD, RMSF plotting was done but I want to compare native and mutant structures through secondary structure element...
08 September 2019 6,145 6 View
