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

[Mark Abraham]

Justin A. Lemkul wrote:
> 
> 
> 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.

Strictly, the problem is that .xvg files written by (at least) g_energy 
assume the dimensions of the ordinate are energy, even if there's only 
one plot and that assumption isn't true. If it bothers you, then you can 
open the text file and correct it by hand (note the gibberish markup in 
kJ/mol that creates superscripts etc.), or write a script to automate 
that with sed.

Mark

>> 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
>>
>