[gmx-users] g_msd and diffusion coefficent

[Justin A. Lemkul]

leila karami wrote:
> Hi gromacs users
>  
> I did simulation of pr-dna by gromacs. I want to obtain diffusion 
> coefficent of pr to dna. I raed manual (g_msd) in which there are  
> diffusion coefficent only for 1 and 2 dimension as follows respectively :
> 
> -type : Compute diffusion coefficient in one direction: no, x, y or z
> 
> -lateral : Calculate the lateral diffusion in a plane perpendicular to: 
> no, x, y or z
> 
> how to use g_msd for calculation of diffusion coeffcient in 3D.

Do not use either of these flags.

-Justin

>  
> Thanks a lot in advance.
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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