[gmx-users] Permeability coefficient

Justin A. Lemkul jalemkul at vt.edu
Wed Sep 7 19:18:31 CEST 2011

manoj gadhwal wrote:
> Dear friends,
> I am using the GROMACS-4.5.3 for molecular dynamics as described 
> by* Justin Lemkul in Tutorial 2: KALP15 in DPPC. *I want to calculate 
> the Permeability Coefficient for Ligand in DPPC so please help me.

I briefly looked up this term and it sounds like you need a diffusion constant 
(which you can get with g_msd) and a partitioning coefficient (which is harder 
to get, but can be obtained from free energy calculations).



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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