[gmx-users] Re:What does this message mean?

Bao Kai paeanball at gmail.com
Tue Jun 5 16:26:55 CEST 2012

Hi, Mark,

Following please find the information.

pure_water]$ g_energy_d -f step11.edr
                         :-)  G  R  O  M  A  C  S  (-:

                      GROwing Monsters And Cloning Shrimps

                            :-)  VERSION 4.5.5  (-:

        Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
      Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
        Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
           Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
                Michael Shirts, Alfons Sijbers, Peter Tieleman,

               Berk Hess, David van der Spoel, and Erik Lindahl.

       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
            Copyright (c) 2001-2010, The GROMACS development team at
        Uppsala University & The Royal Institute of Technology, Sweden.
            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_d (double precision)  (-:

Option     Filename  Type         Description
  -f     step11.edr  Input        Energy file
 -f2       ener.edr  Input, Opt.  Energy file
  -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
-odh       dhdl.xvg  Output, Opt. xvgr/xmgr file

Option       Type   Value   Description
-[no]h       bool   no      Print help info and quit
-[no]version bool   no      Print version 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
-xvg         enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
-[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
-nbmin       int    5       Minimum number of blocks for error estimate
-nbmax       int    5       Maximum number of blocks for error estimate
-[no]mutot   bool   no      Compute the total dipole moment from the
-skip        int    0       Skip number of frames between data points
-[no]aver    bool   no      Also print the exact average and rmsd stored in
                            the energy frames (only when 1 term is requested)
-nmol        int    1       Number of molecules in your sample: the energies
                            are divided by this number
-[no]driftcorr bool no      Useful only for calculations of fluctuation
                            properties. The drift in the observables will be
                            subtracted before computing the fluctuation
-[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 indicates
                            none): 0, 1, 2 or 3
-fitfn       enum   none    Fit function: none, exp, aexp, exp_exp, vac,
                            exp5, exp7, exp9 or erffit
-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 until the end

Opened step11.edr as double 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  LJ-(SR)          2  Disper.-corr.    3  Coulomb-(SR)     4  Coul.-recip.
  5  Potential        6  Kinetic-En.      7  Total-Energy     8  Temperature
  9  Pres.-DC        10  Pressure        11  Box-X           12  Box-Y
 13  Box-Z           14  Volume          15  Density         16  pV
 17  Enthalpy        18  Vir-XX          19  Vir-XY          20  Vir-XZ
 21  Vir-YX          22  Vir-YY          23  Vir-YZ          24  Vir-ZX
 25  Vir-ZY          26  Vir-ZZ          27  Pres-XX         28  Pres-XY
 29  Pres-XZ         30  Pres-YX         31  Pres-YY         32  Pres-YZ
 33  Pres-ZX         34  Pres-ZY         35  Pres-ZZ         36  #Surf*SurfTen
 37  Box-Vel-XX      38  Box-Vel-YY      39  Box-Vel-ZZ      40  Mu-X
 41  Mu-Y            42  Mu-Z            43  T-System        44  Lamb-System


Back Off! I just backed up energy.xvg to ./#energy.xvg.3#
Last energy frame read 1000 time 1000.000

Statistics over 1000001 steps [ 0.0000 through 1000.0000 ps ], 3 data sets
All statistics are over 200001 points

Energy                      Average   Err.Est.       RMSD  Tot-Drift
Temperature                 317.954      0.055    5.75871   0.187709  (K)
Pressure                    100.523       0.21    406.025  0.0312674  (bar)
Density                     967.417       0.16     8.5886   0.992783  (kg/m^3)

You may want to use the -driftcorr flag in order to correct
for spurious drift in the graphs. Note that this is not
a substitute for proper equilibration and sampling!

WARNING: nmol = 1, this may not be what you want.

Temperature dependent fluctuation properties at T = 317.954.

Heat capacities obtained from fluctuations do *not* include
quantum corrections. If you want to get a more accurate estimate
please use the g_dos program.

WARNING: Please verify that your simulations are converged and perform
a block-averaging error analysis (not implemented in g_energy yet)

M. P. Allen and D. J. Tildesley
Computer simulation of liquids
Oxford Science Publications 1 (1987) pp. 1
-------- -------- --- Thank You --- -------- --------

gcq#74: "Baseball Heroes Only" (P.J. Harvey)

Thank you.

On 5/06/2012 10:51 PM, Bao Kai wrote:
> Hi, all,
> It is very easy for me to get the following message.
> WARNING: nmol = 1, this may not be what you want.
> Temperature dependent fluctuation properties at T = 317.98.
> I am wondering if somebody can tell me what does it mean or if it is a
> problem to improve?

We can't possibly know if you won't tell us how you generated this
message, no matter how easy you think it is to generate :-)


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