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

Mon Oct 10 20:15:46 CEST 2016

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?

Thanks a lot,

Jones

On Mon, Oct 10, 2016 at 12:55 PM, Jones de Andrade <johannesrs at gmail.com>
wrote:

> Hi Justin.
>
> Thanks for the answer, sorry for the delay in answering.
>
> That is the point: usualy, I remember g_energy giving me a list of
> properties and energy contributions to be calculated, which I would select
> by an index number. I'm not getting this list nor the program waits for
> such input anymore, so how can I "select the correct energy terms" so that
> the fluctuation properties get calculated?
>
> Thanks a lot for any help,
>
> Jones
>
>
>
> On Fri, Oct 7, 2016 at 11:54 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 10/7/16 6:23 PM, Jones de Andrade wrote:
>>
>>> Hi all.
>>>
>>> I'm having a difficulty using gmx energy.
>>>
>>> My systems are mixtures of 1000 molecules A and 1000 molecules B.
>>>
>>> Concerning gmx energy: I'm using it with the "-fluct_props" flag, but I
>>> really cannot find its output. It only gives me the following:
>>>
>>> Enter the box volume (nm^3):
>>> 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                         154816         11     630.85   -46.9919
>>> (kJ/mol)
>>> Pressure                   -1074.73        7.7    285.913    28.2115
>>> (bar)
>>>
>>> Also, besides the "fluct_props", where is "all the rest" gmx_energy used
>>> to
>>> provide back? Statistics on different energy contributions and everything
>>> else?
>>>
>>>
>> This is exactly what you should expect and is what gmx energy has always
>> printed.  With respect to -fluct_props, I quote the help information:
>>
>> "Some fluctuation-dependent properties can be calculated provided the
>> correct
>> energy terms are selected, and that the command line option -fluct_props
>> is
>> given. The following properties will be computed:
>> Property                        Energy terms needed
>> ---------------------------------------------------
>> Heat capacity C_p (NPT sims):    Enthalpy, Temp
>> Heat capacity C_v (NVT sims):    Etot, Temp
>> Thermal expansion coeff. (NPT): Enthalpy, Vol, Temp
>> Isothermal compressibility:     Vol, Temp
>> Adiabatic bulk modulus:         Vol, Temp
>> ---------------------------------------------------"
>>
>> Since you selected none of those terms, none of the fluctuation-dependent
>> properties are calculated.
>>
>> "Rest" energies are only relevant when using energygrps, where "rest"
>> refers to anything not specified in one of the groups.
>>
>> -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
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
>