[gmx-users] regarding em potential energy positive

[Mark Abraham]

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