[gmx-users] Density of POPC membrane and lateral diffusion

Smith, Iris smithi4 at ccf.org
Tue Aug 21 13:50:09 CEST 2018

Good Morning GROMACS users,

I recently ran a 20 ns production run for my protein-membrane system (POPC).

I calculated the density of the membrane and lateral diffusion of lipids for my system and I have a couple of questions. I ran a short production run to test if my system was stable enough, so I’m not sure if it’s long enough to measure these two key parameters.

  1.  For the density of the membrane, it appears that my water is not distributed evenly and that I may have PBC issues due to asymmetry (lipids jumping). I added a layer of water at the bottom of my box – could it be that I did not add enough water which is causing my lipids to jump?

  1.  For lateral diffusion, I’m not sure if the value (see below) is representative of the diffusion coefficient of POPC in water given the short simulation – should the system be run longer in order to achieve an appropriate value?

$ gmx msd -s md_20.tpr -f md_20.xtc -n p.ndx -lateral z


Selected 22: 'P'
Last frame      10000 time 20000.000

Used 2001 restart points spaced 10 ps over 20000 ps

Fitting from 2000 to 18000 ps

D[         P] 0.007966 (+/- 0.001864) 1e-5 cm^2/s

Thank you, Iris


Iris Nira Smith  |  Postdoctoral Fellow |  Genomic Medicine Institute
Cleveland Clinic  |  9500 Euclid Ave. / NE5-255  |  Cleveland, OH 44195  | (216) 445-7885


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