I re-opened -- just to have this recorded -- but the remaining issue is priority 2 (or maybe even 1) rather than 5.

In Zephyr7.3 on the mac not the entire log is saved to the file zephyr.log. A few lines at the end are missing.

Below an example of log versus Zephyr.log:

zephyr.log file (pasted everything starting with last line
Step = , Time = (line))

============================
GMX: Step = 47792 , Time = 95.584 ps
GMX:
GMX: Writing final coordinates.
GMX:
GMX: NODE (s) Real (s) (%)
GMX: Time: 21.000 21.000 100.0
GMX: (Mnbf/s) (MFlops) (ns/day) (hour/ns)
GMX: Performance: 0.000 0.000 411.429 0.058
GMX:
GMX: gcq#27: "Torture You.... Yeah, That's a Good Idea, I Like That." (Pulp Fiction)
GMX:
GMX: Closing socket connection to VMD...
ZEPHYR/GMX:
Program mdrun completed.
==========================================


Corresponding Log Window (starting from same point)
==========================================
Step = 47792 , Time = 95.584 ps

Writing final coordinates.

NODE (s) Real (s) (%)
Time: 21.000 21.000 100.0
(Mnbf/s) (MFlops) (ns/day) (hour/ns)
Performance: 0.000 0.000 411.429 0.058

gcq#27: "Torture You.... Yeah, That's a Good Idea, I Like That." (Pulp Fiction)

Closing socket connection to VMD...

Program mdrun completed.

Step Time Lambda
50000 100.00001 0.00000

Writing checkpoint, step 50000 at Fri May 1 17:37:39 2009

<====== ############### ==>
<==== A V E R A G E S ====>
<== ############### ======>

Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00
Coulomb-14 LJ (SR) Coulomb (SR) Potential Kinetic En.
0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00
Total Energy Temperature Pressure (bar)
0.00000e+00 0.00000e+00 0.00000e+00

Total Virial (kJ/mol)
0.00000e+00 0.00000e+00 0.00000e+00
0.00000e+00 0.00000e+00 0.00000e+00
0.00000e+00 0.00000e+00 0.00000e+00

Pressure (bar)
0.00000e+00 0.00000e+00 0.00000e+00
0.00000e+00 0.00000e+00 0.00000e+00
0.00000e+00 0.00000e+00 0.00000e+00

Total Dipole (Debye)
0.00000e+00 0.00000e+00 0.00000e+00

<====== ############################### ==>
<==== R M S - F L U C T U A T I O N S ====>
<== ############################### ======>

Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00
Coulomb-14 LJ (SR) Coulomb (SR) Potential Kinetic En.
0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00
Total Energy Temperature Pressure (bar)
0.00000e+00 0.00000e+00 0.00000e+00

Total Virial (kJ/mol)
0.00000e+00 0.00000e+00 0.00000e+00
0.00000e+00 0.00000e+00 0.00000e+00
0.00000e+00 0.00000e+00 0.00000e+00

Pressure (bar)
0.00000e+00 0.00000e+00 0.00000e+00
0.00000e+00 0.00000e+00 0.00000e+00
0.00000e+00 0.00000e+00 0.00000e+00

Total Dipole (Debye)
0.00000e+00 0.00000e+00 0.00000e+00


M E G A - F L O P S A C C O U N T I N G

RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free Energy
T=Tabulated W3=SPC/TIP3p W4=TIP4p (single or pairs)
NF=No Forces

Computing: M-Number M-Flops % Flops
-----------------------------------------------------------------------
Calc-Ekin 0.000032 0.001 19.2
Shake 0.000101 0.003 67.2
Constraint-V 0.000034 0.000 6.0
Shake-Init 0.000034 0.000 7.5
-----------------------------------------------------------------------
Total 0.005 100.0
-----------------------------------------------------------------------


R E A L C Y C L E A N D T I M E A C C O U N T I N G

Computing: Nodes Number G-Cycles Seconds %
-----------------------------------------------------------------------
Write traj. 1 1000 0.038 0.0 0.1
Rest 1 45.542 21.0 99.9
-----------------------------------------------------------------------
Total 1 45.580 21.0 100.0
-----------------------------------------------------------------------

NODE (s) Real (s) (%)
Time: 21.000 21.000 100.0
(Mnbf/s) (MFlops) (ns/day) (hour/ns)
Performance: 0.000 0.000 411.429 0.058
Finished mdrun on node 0 Fri May 1 17:37:39 2009
==========================================

Finished in svn revision 172