I did the following:
- using charmm41, I ran the first script (no efie) five times - simulations were identical, and seed values were identical; when running a second script (with efie) I got different seed values in comparison to the first script, and again, running the second script five times led to identical seed values and identical dynamics;
-using charmm41, I changed the seed myself for all simulations - I get identical dynamics results for all five runs of the first script and identical simulations for all five runs of the second script;
- using charmm37, the results were the same, I even made five identical scripts and run them and got identical results.
In all the scripts I read the same .crd and restart file written after a short equilibration dynamics. Is this the explanation, that velocities are red from the .rst and are the same for all runs?