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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