[gmx-users] Problem with incorrect GB-Polarization Energy Value

[jesmin jahan]

Dear All,

I am using Gromacs 4.5.3 for GB-Polarization Energy Calculation. As I
am not interested to any other energy terms right now, I have set all
the non-bonded parameters to 0.

I am also calculating GB polarization energy using other available
Molecular Dynamic Packages and doing a comparative study between them
(say: Accuracy Vs. Speed Up).
I have already used Gromacs for calculating GB-energy for 168
different Protein molecules and the energy values reported were more
or less the same as reported by others.

Now, I am using a virus shell as input in this process. It contains
1.5 million atoms. Unfortunately, this time, the energy reported is
almost half of the value reported by others.
So, I am a little bit confused. Am I doing something wrong? I have
heard previously that there is no max size for Gromacs.


If anyone have encountered similar kind of problem or have knowledge
about this, please let me know.

Thanks,
Jesmin



-- 
Jesmin Jahan Tithi
PhD Student, CS
Stony Brook University, NY-11790.