[gmx-users] regarding em potential energy positive

[Mark Abraham]

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.

Mark