[AMBER] Regarding MSD calculations in ptraj

From: DEBOSTUTI GHOSHDASTIDAR <debostutighosh.gmail.com>
Date: Fri, 15 Mar 2013 16:02:32 +0530

Dear Amber users,

I have a system comprising of dna dodecamer in a box of water (8000 water
molecules). When I calculate the diffusion coefficient of water in this
system, I get a value of 0.027x10^-9, which is two orders of magnitude
slower than the experimental value. I directly plotted the data of
water_a.xmgr output, calculated the slope and multiplied by 10/6. Am I
missing something here.

Thanks in advance for any suggestions. 

-- 
Debostuti Ghosh Dastidar
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 15 2013 - 04:00:02 PDT
Custom Search