[gmx-users] Wrong Diffusion/Compressibility for Coarse-grained Water
X.Periole at rug.nl
Sun Jul 2 12:49:29 CEST 2006
All time related observables have to scaled by a factor
of 4 in the CG. This was originaly derived from the
diffusion porperties of Water an lipids. You've found it
yourself on the water diffusion.
University of Groningen
> I am trying to get my feet wet with the Coarse-grained
> developed by Marrink et al.
> I've downloaded the examples of top-File, gro-file and
>mdp-file for the
> Water model on Marrink's website.
> Unfortunately, I didn't succeed to reproduce the
>diffusion constant and
> isothermal compressibility data found in Marrink's
> "Coarse-grained Model for Semi-Quantitative Lipid
>Simulations", J. Phys.
> Chem. B, 2004, 108, 750-760.
> The gro-file contains 1728 W beads.
> I didn't changed the parameters in the mdp-file: 100000
>time Steps of 50
>>From g_energy, I obtained an isothermal compressibility
>>of 1.25x10-5 bar-1
> instead of 6x10-5 bar-1 found by Marrink.
>>From g_msd, I obtained a diffusion constant of 1.5x10-5
>>cm2/s instead of
> 5x10-6 cm2/s found by Marrink.
> The Coarse-grained diffusion constant has to be multiply
>by 4 (a CG Water
> bead representing 4 Water molecule) in order to obtained
>a real diffusion
> constant of 2x10-5 cm2/s...
> Do you have any idea why I am not able to reproduce
> Thank you for your help
> Best Regards
> Pierre Verstraete
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