[email protected] wrote:
I am using gromacs-4.0.5.
Try upgrading to the newest version (4.0.7), and if that does not fix the
problem, please report back with the exact command line, gmxcheck output (on the
.edr file), compilers used, hardware, etc.
-Justin
Thanks.
Quoting XAvier Periole <[email protected]>:
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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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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