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
--
========================================
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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