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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