Dear Gromacs users,
I am trying to perform a simulation for a full capsid using GROMACS 2019. After generating topology of the full capsid using pdb2gmx, I solvated capsid using gmx solvate and add ions using gmx genion. Before production run, I did constant NVT (10 ns) and NPT (10 ns), where heavy atoms of the capsid are restrained. From constant NVT and NPT trjectories, I checked water density inside capsid. It is ~ 0.93 gm/ml. After that, I removed restrain in a stepwise manner.
During production run, I saw sudden decrease of radius of gyration of capsid within first 2-3 step of production run. Radius of gyration decrease from 13.85 nm to 13.75 nm. Water density inside capsid is ~ 1.0 gm/ml. My understanding is that capsid collapse happens due to less number of water molecule inside capsid during equilibration. But, I followed steps mentioned in the lysozyme tutorial. I am confused at this point.
Any kind of advice/ suggestions will be deeply appreciated.
Thanks in advance,
Snehasis Chatterjee