[gmx-users] Is there any option to output interaction energy based on energy groups?

Liu Shiyong liushiyong at gmail.com
Tue Jan 20 22:13:33 CET 2009


      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*

[shiyong at reco temp20090115]$ g_energy -f
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                               :-)  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
-zero        real   0       Subtract a zero-point energy

-[no]sum     bool   no      Sum the energy terms selected rather than
                            them all

-[no]dp      bool   no      Print energies in high precision

-[no]mutot   bool   no      Compute the total dipole moment from the


-[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


-[no]normalize bool yes     Normalize ACF

-P           enum   0       Order of Legendre polynomial for ACF (0
                            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

-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
  5  LJ-14            6  Coulomb-14       7  LJ-(SR)          8  LJ-(LR)
  9  Coulomb-(SR)    10  Coulomb-(LR)    11  Potential       12
 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
 25  Pres-YX-(bar)   26  Pres-YY-(bar)   27  Pres-YZ-(bar)   28
 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
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: syliu at ku.edu (shiyongliu at ku.edu or 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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