[gmx-users] how to calculate diffusion constant of the entire lipid-bilayer

[Sanku M]

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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