[gmx-users] Calculation of parameters

Justin Lemkul jalemkul at vt.edu
Thu Jan 10 20:10:17 CET 2013

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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