[gmx-users] analysis of different groups with g_energy

Mark Abraham Mark.Abraham at anu.edu.au
Mon Jun 9 18:27:48 CEST 2008

Peyman Yamin wrote:
> On Monday 09 June 2008 16:19, Justin A. Lemkul wrote:
> Well, ofcourse I did! otherwise I wouldn't expect any program to know them by 
> itself! the problem is that I say:

Well, there's a lesson here. You should spell out all relevant data - 
like your usage of energy groups in your run input file and your full 
observations of g_energy the first time. We don't read minds here, and 
Justin's assumption of your probable failure to plan for your own 
analysis seems to be borne out by the way most new people approach MD 
simulations :-)

> # g_energy -f ../ener.edr -s ../25ns.tpr -b 23000 -e 25000 -skip 25 -o 
> tot_ener
> and I get:
> Opened ../ener.edr as single precision energy file
>   Select the terms you want from the following list
> -----------------------------------------------------
> Angle           Proper-Dih.     Improper-Dih.   LJ-14
> Coulomb-14      LJ-(SR)         Coulomb-(SR)    Coulomb-(LR)
> RF-excl.        Potential       Kinetic-En.     Total-Energy
> Temperature     Pressure-(bar)  Box-X           Box-Y
> Box-Z           Volume          Density-(SI)    pV
> Vir-XX          Vir-XY          Vir-XZ          Vir-YX
> Vir-YY          Vir-YZ          Vir-ZX          Vir-ZY
> Vir-ZZ          Pres-XX-(bar)   Pres-XY-(bar)   Pres-XZ-(bar)
> Pres-YX-(bar)   Pres-YY-(bar)   Pres-YZ-(bar)   Pres-ZX-(bar)
> Pres-ZY-(bar)   Pres-ZZ-(bar)   #Surf*SurfTen   Pcoupl-Mu-XX
> Pcoupl-Mu-YY    Pcoupl-Mu-ZZ    Mu-X            Mu-Y
> Mu-Z            Coul-SR:OCT-OCT LJ-SR:OCT-OCT   Coul-LR:OCT-OCT
> Coul-LR:OCT-TX1 Coul-14:OCT-TX1 LJ-14:OCT-TX1   Coul-SR:TX1-TX1
> LJ-SR:TX1-TX1   Coul-LR:TX1-TX1 Coul-14:TX1-TX1 LJ-14:TX1-TX1
> T-OCT           T-TX1           Lamb-OCT        Lamb-TX1
> without any notification for choosing a group. 

Actually, that's all the notification you get. You can type a 
newline-delimited list of the energy terms you'd like, and follow it 
with a blank line and g_energy will produce your output. You may also 
like to consult 

Note, however, that "total energy of group X" is not available. That's 
because it isn't calculated, and in the vast majority of cases it 
wouldn't mean anything anyway. You can see a breakdown of the nonbonded 
interactions there, however.

> On the other hand, for instance 
> when I say:
> # g_gyrate -f out.xtc -s ../25ns.tpr
> I get, in a beautiful way:
> Reading file ../25ns.tpr, VERSION 3.3.1 (single precision)
> Reading file ../25ns.tpr, VERSION 3.3.1 (single precision)
> Opening library 
> file /apps/GMX/331-intel64-intelmpi-wc/share/gromacs/top/aminoacids.dat
> Group     0 (      System) has 24476 elements
> Group     1 (         TX1) has    46 elements
> Group     2 (         OCT) has 24430 elements
> Select a group:                 
> Now I don't know why I don't get the same behaviour with g_energy, if at all I 
> should expect such a thing!

It's inconsistent, but probably reflects that a different person wrote 
the two programs.


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