Dear prof. Venable,

thank you for all advices.

One more thing, in the documentation the following was written for LD simulations:

3) For heating, equilibration and analysis runs using

Langevin dynamics:(+)

DYNA LEAP LANGEVIN STRT(*) NSTEP 20000 TIMESTEP 0.001 - IPRFRQ 1000 IHTFRQ 0 IEQFRQ 0 NTRFRQ 0 - IUNREA 30 IUNWRI 31 IUNCRD 50 IUNVEL -1 KUNIT 70 - NPRINT 100 NSAVC 100 NSAVV 0 IHBFRQ 0 INBFRQ 25 - ILBFRQ 1000 RBUFFER 0.0 TBATH 300.0 - hbond-spec nonbond-spec - FIRSTT 300.0 FINALT 300.0 - IASORS 0 IASVEL 1 ISCVEL 0 ICHECW 0 TWINDH 0.0 TWINDL 0.0

(+) Note that the friction coefficients, in units of 1/ps, must first be initialized by filling the array FBETA with the SCALAR command SCALAR FBETA SET (*)
Except for first run, the use STRT in place of RESTART

I do not understand how one can know at which point equilibration phase is done, and production phase starts since it is only one script for both?

All best