VMD-L Mailing List

From: cnu gromacs (cnugromacs_at_gmail.com)
Date: Fri May 13 2011 - 13:50:30 CDT

Hi,

I am trying understand the diffusion of protein in a lipid bilayer.

After I performed NAMD simulation.

To avoid the possible artifacts caused by the lipid bilayer motion, using
PBC wrap for each frame i aligned center of lipid bilayer to the center of
unit cell, and recorded the protein coordinates with the following commands.

pbc wrap -centersel "lipid" -center com -compound res -all
animate write dcd protein.dcd beg 0 end -1 sel $protein

Although the commands worked without any error. It does not seem to be
giving me the transformed coordinates (corrected with lipid bilayer
motion).
The calculated COM of the protein before and after use of pbc wrap is same.
Can any body hint me, What would have gone wrong?

best
Srinivas