GROMACS version: 2023.4
GROMACS modification: No
Hi everyone
I am trying to generate a nanoparticle using 60 chains of a 10-mer ethylene polymer. I have successfully modified the OPLS-AA forcefield and set up a simulated annealing (SA) protocol. However after annealing, the nanoparticle seems to disintegrate during a 4 ns production run.
The workflow of the protocol is as follows:
pdb2gmx —> cubic box (3 nm) ----> solvation -----> add ions ----> equilibriation (100 ps) ----> SA using NPT ensemble (6 ns) -----> production (4 ns)
After production it looks something like this:
The nanoparticle looks fine upto annealing part (till the time I use restraints), however it starts to disintegrate in MD production. Please help me this as I am running SA for the first time.
For reference I am attaching the mdp files, temp_sa. xvg and a jpeg images of the production run here.
sa1.mdp (2.9 KB)
temp.xvg (15.3 KB)
md.mdp (2.7 KB)
topol.top (4.0 KB)