[gmx-users] Wrong Diffusion/Compressibility for Coarse-grained Water

verstraete.p at pg.com verstraete.p at pg.com
Wed Jun 14 10:09:50 CEST 2006

Dear all,

I am trying to get my feet wet with the Coarse-grained Force Field 
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 paper:
"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 Marrink's data?

Thank you for your help

Best Regards

Pierre Verstraete
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