[gmx-users] gmx energy -fluct_rprops (gmx 5.1.2): output?
Jones de Andrade
johannesrs at gmail.com
Mon Oct 10 21:19:53 CEST 2016
Hi Justin.
Holy... :P
Thanks a lot! That gave me the options back! I would never expect the need
to "do one thing at a time". :P
Really, sorry for taking everyone's time and inboxes with such a silly
problem.
Yours,
Jones
On Mon, Oct 10, 2016 at 3:57 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 10/10/16 2:47 PM, Jones de Andrade wrote:
>
>> 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
>>
>>
> You're specifying -vis so gmx energy is doing a viscosity calculation,
> which has pre-baked needs. Do one thing at a time.
>
> -Justin
>
>
> :-) 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
>>>
>>> ==================================================
>>> --
>>> Gromacs Users mailing list
>>>
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>>>
> --
> ==================================================
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
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>
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