[gmx-users] Re:What does this message mean?
Mark Abraham
Mark.Abraham at anu.edu.au
Wed Jun 6 07:37:35 CEST 2012
On 6/06/2012 12:26 AM, Bao Kai wrote:
> 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
> components
> -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
> properties.
> -[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, exp9 or erffit
> -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 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
>
> 10
> 15
> 8
>
>
> 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)
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> 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.
> Kai
>
>
> 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?
Had you made different choices of output quantities, there would be more
output from g_energy, and in that context the value of nmol is relevant.
With your choices it doesn't matter, and I have opened a bug report to
explore whether this output should not appear at all.
Thanks,
Mark
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