[gmx-users] regarding em potential energy positive
priya thiyagarajan
priya.thiyagarajan09 at gmail.com
Wed Mar 21 12:48:10 CET 2012
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..
please help me..
Thanking you,
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