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

XAvier Periole x.periole at rug.nl
Thu Apr 15 10:06:56 CEST 2010

On Apr 15, 2010, at 3:05 AM, Sanku M wrote:

> 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 ?
You are right. use g_rms with the lipid bilayer as a group. And  
removing the COM motion
during the simulation is what you want to do.

The question to answer is: is that meaningful? You probably know what  
you re doing.

> Thanks
> Jagannath
> -- 
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