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

jesmin jahan shraban03 at gmail.com
Mon Aug 27 18:33:33 CEST 2012

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.


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

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