Hi,
Is there any option to output total interaction energy
(without *internal
energy*) based on energy groups?
*g_energy -f r-l_365130_G53a6.minim_traj_withH_0.6.minim_ener.edr*
[shiy...@reco temp20090115]$ g_energy -f
r-l_365130_G53a6.minim_traj_withH_0.6.minim_ener.edr
:-) G R O M A C S
(-:
Gnomes, ROck Monsters And Chili Sauce
:-) VERSION 4.0.2 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) g_energy (-:
Option Filename Type Description
------------------------------------------------------------
-f r-l_365130_G53a6.minim_traj_withH_0.6.minim_ener.edr Input
Energy file: edr ene
-f2 ener.edr Input, Opt. Energy file: edr ene
-s topol.tpr Input, Opt. Run input file: tpr tpb tpa
-o energy.xvg Output xvgr/xmgr file
-viol violaver.xvg Output, Opt. xvgr/xmgr file
-pairs pairs.xvg Output, Opt. xvgr/xmgr file
-ora orienta.xvg Output, Opt. xvgr/xmgr file
-ort orientt.xvg Output, Opt. xvgr/xmgr file
-oda orideva.xvg Output, Opt. xvgr/xmgr file
-odr oridevr.xvg Output, Opt. xvgr/xmgr file
-odt oridevt.xvg Output, Opt. xvgr/xmgr file
-oten oriten.xvg Output, Opt. xvgr/xmgr file
-corr enecorr.xvg Output, Opt. xvgr/xmgr file
-vis visco.xvg Output, Opt. xvgr/xmgr file
-ravg runavgdf.xvg Output, Opt. xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-[no]w bool no View output xvg, xpm, eps and pdb files
-[no]xvgr bool yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-[no]fee bool no Do a free energy estimate
-fetemp real 300 Reference temperature for free energy
calculation
-zero real 0 Subtract a zero-point energy
-[no]sum bool no Sum the energy terms selected rather than
display
them all
-[no]dp bool no Print energies in high precision
-[no]mutot bool no Compute the total dipole moment from the
components
-[no]uni bool yes Skip non-uniformly spaced frames
-skip int 0 Skip number of frames between data points
-[no]aver bool no Print also the X1,t and sigma1,t, only if only 1
energy is requested
-nmol int 1 Number of molecules in your sample: the energies
are divided by this number
-ndf int 3 Number of degrees of freedom per molecule.
Necessary for calculating the heat capacity
-[no]fluc bool no Calculate autocorrelation of energy fluctuations
rather than energy itself
-[no]orinst bool no Analyse instantaneous orientation data
-[no]ovec bool no Also plot the eigenvectors with -oten
-acflen int -1 Length of the ACF, default is half the number of
frames
-[no]normalize bool yes Normalize ACF
-P enum 0 Order of Legendre polynomial for ACF (0
indicates
none): 0, 1, 2 or 3
-fitfn enum none Fit function: none, exp, aexp, exp_exp, vac,
exp5, exp7 or exp9
-ncskip int 0 Skip N points in the output file of correlation
functions
-beginfit real 0 Time where to begin the exponential fit of the
correlation function
-endfit real -1 Time where to end the exponential fit of the
correlation function, -1 is till the end
Opened r-l_365130_G53a6.minim_traj_withH_0.6.minim_ener.edr as single
precision energy file
Select the terms you want from the following list by
selecting either (part of) the name or the number or a combination.
End your selection with an empty line or a zero.
-------------------------------------------------------------------
1 G96Bond 2 G96Angle 3 Proper-Dih. 4
Improper-Dih.
5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 LJ-(LR)
9 Coulomb-(SR) 10 Coulomb-(LR) 11 Potential 12
Pressure-(bar)
13 Vir-XX 14 Vir-XY 15 Vir-XZ 16 Vir-YX
17 Vir-YY 18 Vir-YZ 19 Vir-ZX 20 Vir-ZY
21 Vir-ZZ 22 Pres-XX-(bar) 23 Pres-XY-(bar) 24
Pres-XZ-(bar)
25 Pres-YX-(bar) 26 Pres-YY-(bar) 27 Pres-YZ-(bar) 28
Pres-ZX-(bar)
29 Pres-ZY-(bar) 30 Pres-ZZ-(bar) 31 #Surf*SurfTen 32 Mu-X
33 Mu-Y 34 Mu-Z
35 Coul-SR:chAANDB-chAANDB 36 LJ-SR:chAANDB-chAANDB
37 Coul-LR:chAANDB-chAANDB 38 LJ-LR:chAANDB-chAANDB
39 Coul-14:chAANDB-chAANDB 40 LJ-14:chAANDB-chAANDB
41 Coul-SR:chAANDB-chC 42 LJ-SR:chAANDB-chC
43 Coul-LR:chAANDB-chC 44 LJ-LR:chAANDB-chC
45 Coul-14:chAANDB-chC 46 LJ-14:chAANDB-chC
47 Coul-SR:chC-chC 48 LJ-SR:chC-chC
49 Coul-LR:chC-chC 50 LJ-LR:chC-chC
51 Coul-14:chC-chC 52 LJ-14:chC-chC
53 T-rest
--
Shiyong Liu
Postdoc
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: sy...@ku.edu (shiyong...@ku.edu or liushiy...@ku.edu)
Homepage: http://www.people.ku.edu/~syliu
Lab: http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962
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