PIPL01-Stuck and errors in MD

[LobeliaG]

machine-PIPL01 windows version- TEST_V2_3

Out of 3 combinations, both complexes excluding the APO complex threw errors in MD. Both of the jobs also could not be completed and stayed stuck at 95% and 2% even after restarting and resubmitting the jobs. The APO got completed but did not show up in the data analysis.

Only changes from default made in the parameter before MD were integration algorithm and simulation times-

[chandkc]

For energy groups, we can avoid duplicating the npt_flex.mdp and use pressure coupling as Brendsen.

[chandkc]

Regd. the first error: A multiple energy minimization (in a loop) can be attempted.

[chandkc]

+ for 100 steps run MD with dt=0.001 & constraints OFF with Berendsen (temp and pressure).