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

[Justin Lemkul]

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

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