[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
  5  LJ-14            6  Coulomb-14       7  LJ-(SR)          8
  9  Coul.-recip.    10  Potential       11  Pressure        12
 13  Vir-XY          14  Vir-XZ          15  Vir-YX          16
 17  Vir-YZ          18  Vir-ZX          19  Vir-ZY          20
 21  Pres-XX         22  Pres-XY         23  Pres-XZ         24
 25  Pres-YY         26  Pres-YZ         27  Pres-ZX         28
 29  Pres-ZZ         30  #Surf*SurfTen   31  Mu-X            32
 33  Mu-Z            34  T-rest


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

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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