I created new project, and prepared for simulation by “Gromacs FULL MD setup”.
Using this prepared structure, I ran “Simple Box Solvent Molecular Dynamics (NPT)” 2 times.
After simulation, I noticed that these 2 simulation seeds(written in log file as ld_seed) are same.
But other results (gro, trr, xtc, pdb) were different.
And using analysis tool, I checked RMSd and Bfactor. These were also different.
Then using analysis tool “Get a trajectory snapshot”, I checked structures first step and last step.
These structures were same between first and second simulation.
If seed is same, should simulation results be same?
Can I change seed for simulation?
Trajectories are different, why are snapshots same?
Thank you for your help.