[gmx-users] Calculation of parameters

[Justin Lemkul]

On 1/10/13 1:59 PM, Bharath K. Srikanth wrote:
> Hi
>
> Is it possible to use the GROMACS methods g_msd or g_velacc to calculate
> parameters (i.e the diffusion coefficient) when the parameter value varies
> with position (eg. diffusion of a nanoparticle through a lipid bilayer)?
> If so, how?
>
> If not, are there any other GROMACS methods that can be used to obtain
> this position-dependent diffusion coefficient from a trajectory file?
>

Presumably you should be able to analyze the diffusion during different time 
frames within the trajectory using -b and -e with any command.  That would allow 
you to measure diffusion constants in different environments, assuming you have 
enough data in each environment to make reasonable observations.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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