That looks like a nice bug!
You should specify which gmx version you are using. That would help
getting it fixed.
On Apr 13, 2010, at 21:34, [email protected] wrote:
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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