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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