[gmx-users] How to plot Pressure (bar) vs simulation time in ps

[Justin A. Lemkul]

Lum Nforbi wrote:
> Hi everyone,
> 
> I need to plot a graph of pressure (bar) vs run time (ps) but I am havin 
> problems with this because the graph's y-axis diplays energy (KJmol^-1) 
> instead of pressure. How can I correct this energy on the y-axiz of my 
> plot to pressure (bar)?

Pressure is in bar (hence the average value also printed by g_energy).  The 
problem with is that g_energy prints all its output in kJ/mol.

-Justin

> 
> I have used this command to view the value of my pressure (g_energy -f 
> wfullmdrun_ener.edr -o wfullmdrun_PRESSURE4000ps.xvg) and I choose the 
> pressure in the table below in order to display the value. 
> 
> Select the terms you want from the following list by
> selecting either (part of) the name or the number or a combination.
> End your selection with an empty line or a zero.
> -------------------------------------------------------------------
>   1  LJ-(SR)          2  Coulomb-(SR)     3  Coul.-recip.     4  
> Potential    
>   5  Kinetic-En.      6  Total-Energy     7  Temperature      8  
> Pressure-(bar)
>   9  Box-X           10  Box-Y           11  Box-Z           12  
> Volume       
>  13  Density-(SI)    14  pV              15  Vir-XX          16  
> Vir-XY       
>  17  Vir-XZ          18  Vir-YX          19  Vir-YY          20  
> Vir-YZ       
>  21  Vir-ZX          22  Vir-ZY          23  Vir-ZZ          24  
> Pres-XX-(bar)
>  25  Pres-XY-(bar)   26  Pres-XZ-(bar)   27  Pres-YX-(bar)   28  
> Pres-YY-(bar)
>  29  Pres-YZ-(bar)   30  Pres-ZX-(bar)   31  Pres-ZY-(bar)   32  
> Pres-ZZ-(bar)
>  33  #Surf*SurfTen   34  Mu-X            35  Mu-Y            36  
> Mu-Z         
>  37  T-SOL           38  Lamb-SOL     
> 
> 8 0
> Last energy frame read 20000 time 4000.000          
> 
> Statistics over 2000001 steps [ 0.0000 thru 4000.0002 ps ], 1 data sets
> All averages are exact over 2000001 steps
> 
> Energy                      Average       RMSD     Fluct.      Drift  
> Tot-Drift
> -------------------------------------------------------------------------------
> Pressure (bar)             0.868069    194.562    194.557 0.00116891    
> 4.67564
> 
> 
> Thank you,
> 
> Lum
> 

-- 
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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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