[gmx-users] error in energy minimzation step

[Justin Lemkul]

On 3/3/13 6:44 AM, az kalsom wrote:
> hi ,
>
> while ruuning the COMMAND
>
> g_energy -f em.edr -o potential.xvg
>
> and following the tutorial
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/05_EM.html
>
>   i am getting the following error
>
>
> 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  Bond             2  Angle            3  Proper-Dih.      4
> Ryckaert-Bell.
>    5  LJ-14            6  Coulomb-14       7  LJ-(SR)          8
> Coulomb-(SR)
>    9  Coul.-recip.    10  Potential       11  Pressure        12
> Vir-XX
>   13  Vir-XY          14  Vir-XZ          15  Vir-YX          16
> Vir-YY
>   17  Vir-YZ          18  Vir-ZX          19  Vir-ZY          20
> Vir-ZZ
>   21  Pres-XX         22  Pres-XY         23  Pres-XZ         24
> Pres-YX
>   25  Pres-YY         26  Pres-YZ         27  Pres-ZX         28
> Pres-ZY
>   29  Pres-ZZ         30  #Surf*SurfTen   31  Mu-X            32
> Mu-Y
>   33  Mu-Z            34  T-rest
>
> 10 0
> Last energy frame read 1545 time 1952.000
>
> Statistics over 1953 steps [ 0.0000 through 1952.0000 ps ], 1 data sets
> All statistics are over 1546 points (frames)
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> Potential                -2.30149e+06      39000     520034    -251635
> (kJ/mol)
>
> You may want to use the -driftcorr flag in order to correct
> for spurious drift in the graphs. Note that this is not
> a substitute for proper equilibration and sampling!
> You should select the temperature in order to obtain fluctuation properties.
>
>
>
> please help me , what should i change or do to remove error this error
>

What error?

The average potential energy during EM is also a meaningless quantity, because 
it changes at each step.  A plot of the potential energy will give you an 
indication about convergence, but the average tells you nothing.

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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