[gmx-users] analysis of different groups with g_energy

[Peyman Yamin]

Hi again,

Now I remember! some old g_energy let me use numbers as the input for the 
terms I wanted...!

As you say, it looks like the total energy for different groups is not 
calculated. So I should somehow do it myself? If yes, I don't even know where 
I should get the terms I should add together from? I think I'd need all 
bonding and nonbonding interactions! or I should even calculate them?

I can't also find what SR and LR and 14 mean in energy terms...!

Would greatly appreciate any suggestion,
Peyman  





On Monday 09 June 2008 18:27, Mark Abraham wrote:
> 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-14:OCT-OCT LJ-14:OCT-OCT   Coul-SR:OCT-TX1 LJ-SR:OCT-TX1
> > 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
> http://wiki.gromacs.org/index.php/Making_Commands_Non-Interactive
>
> 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.
>
> Mark
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-- 
Peyman Yamin
Lehrstuhl fuer Thermische Verfahrenstechnik
University of Erlangen
Egerlandstr. 3, 91058 
Erlangen, Germany
peyman.yamin AT cbi.uni-erlangen.de