[gmx-users] analysis of different groups with g_energy

[Peyman Yamin]

Thanks! 

I had somewhere in my mind a memory of seeing an interactive g_energy some 
time ago, but it could be another version of it or that place in my mind 
would need a defragmentation!  comments helped indeed anyway.

If group X is one molecule, you would know from it's energy, i.e. the sum of 
interactions its atoms have with themself and with the surrounding solvent, a 
plenty of useful things. It could, if analysed with an eye on physicochemical 
nature of interactions and the resulting conformers, could give neat insights 
in some cases. e.g. how would one find some attractors about a certain 
arbitrarily defined size-related property, in terms of stability? I thought 
if molecule X is tending to have some conformer with the least energy in 
medium A, it would also be tending to have an alike conformer in some other 
medium of the same nature to the first one.

This is what I think, and, you might want to correct me of course.

But what I don't know now is if the tot-energy output from g_energy when one 
chooses a certain molecule, is actually what I think it is, or it's 
calculated in another way? How would I know?

Regards,
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