Hello,
I am a running a simulation of 100ns, so I have two edr files
md.edr and md.part0002.edr. When I calculate some of the energy values
using g_energy for each of the .edr files individually I get the
following result:
For md.edr:
Statistics over 27120401 steps [ 0.0000 thru 54240.8008 ps ], 4 data sets
All averages are over 271205 frames
Energy Average RMSD Fluct. Drift
Tot-Drift
-------------------------------------------------------------------------------
Temperature 297.996 3.75973 3.75972 6.88223e-07
0.0373298
Pressure (bar) 1.66199 262.287 262.287 -2.24459e-05
-1.21748
Volume 66.1617 0.39728 0.39728 0
0
Density (SI) 983.924 5.90292 5.90292 -1.44217e-07
-0.00782243
Heat Capacity Cv: 12.4747 J/mol K (factor = 0.000159181)
Isothermal Compressibility: 5.79816e-05 /bar
Adiabatic bulk modulus: 17246.9 bar
For md.part0002.edr
Statistics over 22986601 steps [ 54026.8008 thru 100000.0078 ps ], 4 data sets
All averages are over 229867 frames
Energy Average RMSD Fluct. Drift
Tot-Drift
-------------------------------------------------------------------------------
Temperature 297.993 3.75398 3.75397 -5.66217e-07
-0.0260308
Pressure (bar) 1.51511 263.692 263.692 4.88234e-05
2.24457
Volume 66.1617 0.398494 0.39849 1.29794e-07
0.00596703
Density (SI) 983.924 5.9329 5.93284 -1.92684e-06
-0.088583
Heat Capacity Cv: 12.4747 J/mol K (factor = 0.000158697)
Isothermal Compressibility: 5.8337e-05 /bar
Adiabatic bulk modulus: 17141.8 bar
But then when I combined my .edr files using eneconv -f md.edr
md.part002.edr. the output is saved into 'fixed.edr' and when I ran
fixed.edr file through g_energy, I get negative values as follows :
Statistics over 50000001 steps [ 0.0000 thru 100000.0078 ps ], 4 data sets
All averages are exact over 50000001 steps
Energy Average RMSD Fluct. Drift
Tot-Drift
-------------------------------------------------------------------------------
Temperature -5.90251e-06 0 0 0
0
Pressure (bar) 4.46175e-06 0 0
-9.66961e-07 -0.0966961
Volume -1.32585e-06 0 0 0
0
Density (SI) -1.96389e-05 0 0 -2.119e-07
-0.02119
Heat Capacity Cv: 12.4718 J/mol K (factor = 0)
Isothermal Compressibility: 0 /bar
Adiabatic bulk modulus: inf bar
I don't understand what happened there. Could someone please help me
understand if I am combining the files correctly, or it is something I
am missing.
Thanks
Nisha Patel
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