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

[Yang Ye]

5 days for 45ns. how big is your system? and what parameters you have 
set for electrostatic/vdw calculation?

Yang Ye

Marino Convertino wrote:
> 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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-- 
/Regards,/
Yang Ye
/Computational Biology Lab
School of Biological Sciences
Nanyang Technological University
Singapore
Tel: 6316-2884
/