[gmx-users] Is there any option to output interaction energy based on energy groups?
David van der Spoel
spoel at xray.bmc.uu.se
Wed Jan 21 09:03:57 CET 2009
Liu Shiyong wrote:
> Hi,
>
> Is there any option to output total interaction energy (without
> *internal energy*) based on energy groups?
If you can divide your system based on a few groups that are not
covalently bound (i.e. no bonds, angles, dihedrals) then it will work
easily for the short-range LJ and Coulomb. For PME it is more difficult.
Please search the archives, for PME interaction energy.
>
>
> *g_energy -f r-l_365130_G53a6.minim_traj_withH_0.6.minim_ener.edr*
>
> [shiyong at 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: syliu at ku.edu <mailto:syliu at ku.edu> (shiyongliu at ku.edu
> <mailto:shiyongliu at ku.edu> or liushiyong at ku.edu <mailto:liushiyong at ku.edu>)
> Homepage: http://www.people.ku.edu/~syliu
> Lab: http://vakser.bioinformatics.ku.edu/people
> Phone: (785) 864-1962
>
>
> ------------------------------------------------------------------------
>
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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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