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

[Smith, Iris]

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



[/Users/smithi4/Library/Containers/com.microsoft.Outlook/Data/Library/Caches/Signatures/signature_1451095126]

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




===================================


 Please consider the environment before printing this e-mail

Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.