VMD-L Mailing List

From: Alex Liu (liu.alex77_at_yahoo.com)
Date: Tue Nov 23 2010 - 09:21:31 CST

Hi all,
I want to take the average structure from a MD trajectory. My system includes a
DNA molecule with some cations in channel which are surrounded with a water box
containing counter ions.
When I unwrap the system, the DNA and the channel ions look like a very small
molecule in a very huge box of water and counter ions which spread far around (I
think because the water molecules and the counter ions move much
faster than DNA).
Now, to find the average structure from unwrapped trajectory, the average
positions for DNA and channel ions make sense while the positions for
water and counter ions are very far from the DNA (just because of the face I
mentioned above). For the similar system from literature I have seen the
distribution of water and counter ions should be around DNA.
What I think is that the approach to take the average structure for solute is
different from the solvent. For example I may need to take the average positions
for DNA and channel ions from unwrapped structure and average positions for
water and counter ions from wrapped one. Is that true or am I missing something?
Thanks,
Alex