[gmx-developers] Fluctuation properties

[Michael Shirts]

> Trying to run as you advertise it (512 TIP4P/PME/LJ-Cut):
> Statistics over 7101 steps [ 5.0000 thru 19.2000 ps ], 2 data sets
> All averages are over 7101 frames
>
> Energy                      Average       RMSD     Fluct.  Tot-Drift
> -------------------------------------------------------------------------------
> Total Energy               -17316.8    169.118    154.362   -239.337
> (kJ/mol)
> Conserved En.              -17304.4    7.48269    1.90526    25.0665
> (kJ/mol)
>
> Is this as expected?

In terms of the conserved quantity -- hard to say,  LJ-Cut probably
isn't helping conserve the conserved quantity that much; a continuous
shift or switch as Berk suggests would be better.  MTTK is volume
preserving and time reversible, but not symplectic, so the conserved
quantity has time average zero, but is not strictly flat.


> And another point: is this supposed to run in parallel? It runs fine on
> 1 cpu but gives me a SEGV on 4 cores...

It is!  Are you using the latest version?  I checked in some parallel
fixes a couple of days ago.  If it -is- fresh, and is still breaking,
please email me the setup files so I can verify them and fix it.
Perhaps there's something that should be initialized that goes through
fine on my test systems, but doesn't work on this system.