[gmx-users] gmx energy -fluct_rprops (gmx 5.1.2): output?
Jones de Andrade
johannesrs at gmail.com
Mon Oct 10 20:48:00 CEST 2016
Hi JUstin.
Thanks for the reply: my full command line and output screen follows.
***********
$ date
Mon Oct 10 15:42:06 BRT 2016
$ gmx energy -f 1000.BMIm.AlCl4.md.020.edr -o
1000.BMIm.AlCl4.md.020.energy.xvg -vis
1000.BMIm.AlCl4.md.020.energy.visenergy.xvg -fluct_props -driftcorr -nmol
1000
:-) GROMACS - gmx energy, VERSION 5.1.2 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par
Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch
Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent Hindriksen
Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten
Kutzner
Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff
Erik Marklund Teemu Murtola Szilard Pall Sander Pronk
Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx energy, VERSION 5.1.2
Executable: /opt/versatushpc/softwares/gromacs/5.1-gnu-4.8/bin/gmx
Data prefix: /opt/versatushpc/softwares/gromacs/5.1-gnu-4.8
Command line:
gmx energy -f 1000.BMIm.AlCl4.md.020.edr -o
1000.BMIm.AlCl4.md.020.energy.xvg -vis
1000.BMIm.AlCl4.md.020.energy.visenergy.xvg -fluct_props -driftcorr -nmol
1000
Opened 1000.BMIm.AlCl4.md.020.edr as single precision energy file
Enter the box volume (nm^3): 2500
Back Off! I just backed up 1000.BMIm.AlCl4.md.020.energy.xvg to
./#1000.BMIm.AlCl4.md.020.energy.xvg.6#
Last energy frame read 100000 time 40000.000
Statistics over 1000001 steps [ 38000.0000 through 40000.0000 ps ], 12 data
sets
All statistics are over 100001 points (frames)
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
Pres-XX -1074.79 14 409.963 26.7157 (bar)
Pres-XY -8.27597 5.7 252.371 18.7887 (bar)
Pres-XZ 6.33249 5 252.304 25.7754 (bar)
Pres-YX -8.27612 5.7 252.371 18.7888 (bar)
Pres-YY -1064.35 7.6 404.26 -0.442493 (bar)
Pres-YZ -2.17376 2 249.215 -7.94723 (bar)
Pres-ZX 6.33449 5 252.304 25.7753 (bar)
Pres-ZY -2.17351 2 249.216 -7.94715 (bar)
Pres-ZZ -1085.03 11 408.913 58.3614 (bar)
Temperature 298.001 0.0022 1.62607 0.000771545 (K)
Bond 154.816 0.011 0.63085 -0.0469919
(kJ/mol)
Pressure -1074.73 7.7 285.913 28.2115 (bar)
Back Off! I just backed up eviscoi.xvg to ./#eviscoi.xvg.5#
Back Off! I just backed up evisco.xvg to ./#evisco.xvg.5#
Back Off! I just backed up enecorr.xvg to ./#enecorr.xvg.10#
Back Off! I just backed up enecorr.xvg to ./#enecorr.xvg.11#
Back Off! I just backed up 1000.BMIm.AlCl4.md.020.energy.visenergy.xvg to
./#1000.BMIm.AlCl4.md.020.energy.visenergy.xvg.6#
Temperature dependent fluctuation properties at T = 298.001.
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#459: "We are perhaps not far removed from the time when we shall be
able to submit the bulk of chemical phenomena to calculation." (Joseph
Gay-Lussac, 1808)
$
***********
As you can see, there is both no list of options nor waiting prompt for
them in my output. :(
Looking forward for any help on this matter,
Thanks a lot,
Jones
On Mon, Oct 10, 2016 at 3:23 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 10/10/16 2:15 PM, Jones de Andrade wrote:
>
>> Just an addendum:
>>
>> I used to get *this* kind of output out of g_energy (not "gmx_energy", my
>> mistake):
>>
>> **************
>> 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 Coulomb-(SR) 3 Position-Rest. 4 Potential
>> 5 Kinetic-En. 6 Total-Energy 7 Conserved-En. 8 Temperature
>> 9 Pressure 10 Constr.-rmsd 11 Vir-XX 12 Vir-XY
>> 13 Vir-XZ 14 Vir-YX 15 Vir-YY 16
>> Vir-YZ
>> 17 Vir-ZX 18 Vir-ZY 19 Vir-ZZ 20
>> Pres-XX
>> 21 Pres-XY 22 Pres-XZ 23 Pres-YX 24 Pres-YY
>> 25 Pres-YZ 26 Pres-ZX 27 Pres-ZY 28 Pres-ZZ
>> 29 #Surf*SurfTen 30 Mu-X 31 Mu-Y 32 Mu-Z
>> 33 T-System
>> ***********
>>
>> This was what gave me a way to select properties to be calculated. It
>> *does
>> not* appears in gmx_energy. How can I select properties now? What am I
>> doing wrong?
>>
>>
> Absent your exact command and full screen output, there's nothing to go
> on. I get the expected list in 5.1. Nothing should have changed with
> respect to energy output selections in any recent version.
>
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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