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

[Jones de Andrade]

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.
>