1. The molecules are the same. But we built the system in different method, and used different number of molecules.
2. We both used the oplsaa all-atom force field, but the parameters are a little different.
3. I used gromacs. The reference used MDynaMix.
4. The unit of energy are both KJ/mol
I think no matter what softwares or systems, the energies should almost the same. At least, they should not deviate to much? is it right?
PS: For the pressure, I used Berendsen pressure coupling.
2006/9/21, Dallas B. Warren <[EMAIL PROTECTED]
>:
>1. I simualted a pure small molecule system. All the simulation is ok.
But
>when I use g_energy to calculate the energy of bond, angle, lj, and
coloumb,
>it gives the following energy. The energies is much bigger, about
50-100 times
>bigger than the reported data. What's wrong?
Well, that depends on what the reported data actually is to whether you
can actually make the comparison.
Is it for exactly the same system with the same forcefield?
Is it for the entire system or for per molecule?
Catch ya,
Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
[EMAIL PROTECTED]
+61 3 9903 9524
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail.
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Sincerely yours,
**********************************************
Baofu Qiao, PhD
Frankfurt Institute for Advanced Studies
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