i am facing a problem while running MD simulation of my system. i set the ensemble as NPT to identify the density. Then I changed to NVT with new density with same desired temperature. I found that during simulation the temperature is dropped from 373.15K to 100K.
Same density!!
Did you keep box lengths same as in the final NPT .gro file?
I would rather suggest you to do the following
grompp -f nvt.mdp -c npt.gro -t npt.cpt -p system.top -o npt.tpr
then try to run the simulation.
I'm assuming that you have properly equilibrated (energy, volume, temperature) your system prior to this NVT run.
all the best.
This is unusual situation, I will suggest you to check the system relaxation, or the boundary situation, or if there is any structure conflict... You could check the output file of our initial NPT calculation or the input file of your NVT calculation, expecially the term related to momentum of each atom.
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