[gmx-users] how to calculate diffusion constant of the entire lipid-bilayer
Sanku M
msanku65 at yahoo.com
Thu Apr 15 03:05:29 CEST 2010
Hi,
I was interested in calculating the diffusion constant of the center of mass of entire lipid-bilayer ( not individual lipid molecules). Regarding this, I had two doubts I wanted to clarify:
1. Since I am interested in calculating the diffusion constant of the bilayer iteself, I guess I should allow the drift of the bilayer and hence not then remove the center of mass motion of bilayer (and solvent ) separately. Is that right ? If so, is it still OK to remove the center of mass of whole system ( bilayer + water together ) ?
2. How to calculate the mean square displacement of center of mass of the entire bilayer. I guess, g_msd program by default, calculate the diffusion constant of the individual atoms or molecules. But, is there a way to get the diffusion constant of the entire bilayer center of mass ? If I specify the index group which consist of all the atoms of the bilayer, will g_msd provide the diffusion constant of its center of mass or it will give the diffusion constant of individual atoms ? I guess, in that case, one should not use -rmcomm option . Is that right ?
Thanks
Jagannath
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