[gmx-users] Re: Re: Re: temperature and pressure values

[Marino Convertino]

Dear Mark and all,
Sorry for boring you again.
I have performed a g_energy check.
Firstly I use a 45ps NPT equilibration with costrained protein then another 45ps NPT equilibration with free protein.
Now I am studying a 350k full dynamics of the same system.
These are the g_energy results:

For the first equilibration:
Statistics over 30001 steps [ 0.0000 thru 45.0000 ps ], 3 data sets

Energy                      Average       RMSD     Fluct.      Drift  Tot-Drift
-------------------------------------------------------------------------------
Total Energy                -332261    2534.56    1997.14    -120.13   -5406.05
Temperature                 353.591    1.91115    1.89532  0.0188968   0.850383
Pressure (bar)             -26.2488      132.2    124.656    3.38837    152.482
Heat Capacity Cv:      12.4723 J/mol K (factor = 2.92137e-05)

For the second equilibration:
Statistics over 30001 steps [ 0.0000 thru 45.0000 ps ], 3 data sets

Energy                      Average       RMSD     Fluct.      Drift  Tot-Drift
-------------------------------------------------------------------------------
Total Energy                -333296    405.704    402.837    3.70631    166.789
Temperature                 353.436     1.3876    1.38391 0.00778066   0.350141
Pressure (bar)              1.51139    98.9854    98.9833 -0.0503028    -2.2637
Heat Capacity Cv:      12.4721 J/mol K (factor = 1.54138e-05)


For full dynamics (45ns) after 5-days-computing time: 
Statistics over 5617501 steps [ 0.0000 thru 8426.2500 ps ], 3 data sets

Energy                      Average       RMSD     Fluct.      Drift  Tot-Drift
-------------------------------------------------------------------------------
Total Energy                -333496    458.834    457.266  0.0155822    131.299
Temperature                 353.429    1.39732    1.39731 2.05578e-06  0.0173225
Pressure (bar)              1.02358    99.7865    99.7842 -0.000278171   -2.34394
Heat Capacity Cv:      12.4721 J/mol K (factor = 1.56309e-05)

Would you think they are ok?
Can I consider satisfactory the average values of temperature and pressure?
If not, I will try to follow your previous suggestions adding two NVT equilibration steps (before the NPT ones, because the EM steps worked fine).

Thanks a lot 
Marino



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