[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
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?
>
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 :-)
Mark
More information about the gromacs.org_gmx-users
mailing list