On 21/03/2012 10:53 PM, Mark Abraham wrote:
On 21/03/2012 10:48 PM, priya thiyagarajan wrote:
hello sir,
initially i did dynamics for my protein with 30000water molecules..
it went correctly..
when i thought of reducing water i decreased my box size so that my
sol number is around 70000.
when i go for energy minimisation i got its output.. but when i
analysed its potential energy its coming as positive..
even i tried many times but i am getting positive energy ..
to have a stable system i need to have negative PE..
this is my analysis outut
Opened surf_em.edr as single precision energy file
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 G96Bond 2 G96Angle 3 Proper-Dih. 4
Improper-Dih.
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
Back Off! I just backed up energy.xvg to ./#energy.xvg.1#
Last energy frame read 276 time 347.000
Statistics over 347 steps [ 1.0000 through 347.0000 ps ], 1 data sets
All statistics are over 277 points (frames)
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
Potential 270008 250000 1.01247e+06
-1.51432e+06 (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.
gcq#336: "Ohne Arbeit wird das Leben Oede" (Wir Sind Helden)
can anyone please help me why its coming like this..
i am got negative value when i did initially with 300000 sol.. but
now getting positive value for 70000sol..
It seems wildly unlikely that the only difference in your procedure is
the size of the box and thus the number of water molecules. However,
until you can document that procedure, nobody can know.
I assumed that the positive average value indicated that your
problematic system always had a positive PE - but as Justin has
suggested you should look at a more useful indicator of correct behaviour.
Mark
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