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How atom are named in .pdb file?
5. How to run energy minization(potential) step for longer time?
6. How much time run is good for NVT and NPT equilibriation steps? How to make temperature, pressure and density fluctuation minimum?
7. How much fluctuation in temerature, pressure and density is good for MD run ?
increase nsteps in mdp file.
It depends on your system. It is better to look at articles with similar system. But, for npt it depends on time your system needs to reach equilibration( you can use ACF to get it).
The kind of termostat and barostat you use and also their (tau) determine flactuations.
This is not necessarily true, nor is it necessarily necessary. Energy minimization is not a dynamical process, and it terminates when the convergence criteria are met. So, if you reach a maximum force below emtol or the minimizer can’t make any change to the energy, it will stop, regardless of what you have set for nsteps.
Dear jalemkul
You are right. Thank you for your correction.
best,
thank you