[gmx-users] question about energy and pressure

[Qiao Baofu]

Hi Dallas Warren,

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 <Dallas.Warren at vcp.monash.edu.au>:
>
> >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
> dallas.warren at vcp.monash.edu.au
> +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
Max-von-Laue-Str. 1
60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529
**********************************************
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