[gmx-users] question about energy and pressure

Qiao Baofu qiaobf at gmail.com
Thu Sep 21 09:14:08 CEST 2006

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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