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