[gmx-users] analysis of different groups with g_energy

Peyman Yamin Peyman.Yamin at cbi.uni-erlangen.de
Mon Jun 9 16:39:51 CEST 2008

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:

# g_energy -f ../ener.edr -s ../25ns.tpr -b 23000 -e 25000 -skip 25 -o 

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. 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!


> Choose appropriate energygrps in your .mdp file.
> -Justin
> Peyman Yamin wrote:
> > Dear Gromacs users,
> >
> > I'm simulating dilute solutions of different surfactants in different
> > media. All I want to analyse afterwards, though, is the single surfactant
> > molecule properties!
> >
> > Is there any way to extract energy data from the original .edr file with
> > respect to a single group, in the same way as one can extract structures
> > from an .xdr with trjconvm?
> > Is there any way to use g_energy to different groups? as I see I can only
> > have some of the properties in a group-specified way - like T! I'm not
> > asked in which group i'm interested and neither I can specify it at
> > command-line, that I want, say total-energy of group G!
> >
> > Thanks in advance,
> >
> > Best regards
> > Peyman

Peyman Yamin
Lehrstuhl fuer Thermische Verfahrenstechnik
Universitaet Erlangen-Nuernberg
Egerlandstr. 3
91058 Erlangen
Phone: +49(0) - 9131 - 85 27671
Mailto: peyman.yamin at cbi.uni-erlangen.de

More information about the gromacs.org_gmx-users mailing list