[gmx-users] gmx energy -fluct_rprops (gmx 5.1.2): output?

Mon Oct 10 20:57:58 CEST 2016

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:
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> 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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-- 
==================================================

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

==================================================