[gmx-users] Ensemble averaged restraints

Hello all, I have read in many papers where restraints have been applied to ensembles of structures and I can theoritically think of that but I am not able to get my head around on how to implement it. Theoretically the method should do this : 1). Once we have N structures that we want to simulate

[gmx-users] g_cluster -dm option

Hello, I am using g_cluster to cluster trajectories. The exact command I am using is : g_cluster -s protein.pdb -f all.trr -n index.ndx -o rmsd-clust.xpm -method gromos -cutoff 0.07 -wcl 250. This command gives me 145 clusters. This command writes out a rmsd-clust.xpm, which is the RMSD distance

[gmx-users] General Question about Simulated Annealing

Hello all, I have read many papers about using simulated annealing protocol along with experimental data. I have some questions about the protocol itself and would really appreciate if some body clears it. The general MD simulation gets the information about forces from FF and starting with initi