I know that there are lots of topics about high RMSD value, sudden jumps or fluctuations. I’ve been scrolling through the topics and trying to apply several trjconv commands into my system but could not even get a smooth RMSD value and I am not sure if my system has crashed. I have carried out protein+ligand MD simulation and I had smooth RMSD values so far except the last system I set up for my simulation. I couldn’t fix my RMSD result even though I have tried several commands that I have listed out of order.
Both frames appear to be simple PBC issues. What group are you choosing for the trjconv selections related to centering and fitting? You should be choosing the protein, or perhaps just the backbone. If you do, the ligand will wrap to the protein.
Your ligand clearly dissociates and it isn’t an artifact. What is the ligand and how did you parametrize it? It looks rather small and very flexible, so it will be extremely sensitive to the quality of the topology you generate for it.
That topology makes no sense at all. The charges are totally wrong, with most of the C and H atoms bearing zero charge. The charged amino and carboxy groups are over-polarized with respect to typical CHARMM groups so altogether it probably renders the molecule wildly imbalanced and prone to dissociation.
You can generate a topology for this species very easily by analogy from existing CHARMM parameters (by analogy to LYS and GLU, from CHARMM36):
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 NH3 1 LIG N 1 -0.3000 14.0067
2 CT2 1 LIG CA 2 0.2100 12.0110
3 CT2 1 LIG CB 3 -0.1800 12.0110
4 CT2 1 LIG CG 4 -0.2800 12.0110
5 CC 1 LIG CD 5 0.6200 12.0110
6 OC 1 LIG OE1 6 -0.7600 15.9994
7 OC 1 LIG OE2 7 -0.7600 15.9994
8 HA2 1 LIG HA2 8 0.0500 1.0079
9 HA2 1 LIG HA3 9 0.0500 1.0079
10 HA2 1 LIG HB2 10 0.0900 1.0079
11 HA2 1 LIG HB3 11 0.0900 1.0079
12 HA2 1 LIG HG2 12 0.0900 1.0079
13 HA2 1 LIG HG3 13 0.0900 1.0079
14 HC 1 LIG H1 14 0.3300 1.0079
15 HC 1 LIG H2 15 0.3300 1.0079
16 HC 1 LIG H3 16 0.3300 1.0079
Thanks for your kind consideration. I did it as a part of molecular docking protocol where I have to add hydrogen. Not sure though if I can avoid protonation of terminal carboxylate while adding polar hydrogen.
Please guide me over it.