In my last molecular dynamics article, we saw:
- formation of GEL state lipids which are very ordered
- interdigitation of upper and lower layer lipids
in the DMPC membrane patch which was simulated(for 320 nanoseconds) at temperature 290K. As illustrated in the below image, we know that the main transition temperature of DMPC membrane is 297K.
Open the image in a separate tab for enlarged version
We also saw the interdigitation plot for this case(290K). But to really prove the fact scientifically, we need a control case. As the transition temperature Tm is 297K, any simulation experiment of DMPC membrane above this temperature must not exhibit
- gel phased lipids and
- interdigitation
So I repeated the same experiment as in my previous article, but with a difference this time. Instead of temperature 290K, I used 310K which is well above 297K. Also, I am only running for 200 nanoseconds to reduce computational cost. This won't affect the results since the system is getting equilibrated by this time as we saw last time. An extra runtime will only costly in this case. I am providing system details below:
SYSTEM (same as in the last article)
- 288 DMPC lipids(144 in upper and lower leaflets each)
- 7776 water molecules
- 12 Sodium and 12 Chloride ions
TOTAL: 57336 atoms
The system was generated using the steps described here using CHARMM-gui tool. - Temperature = 310K
- Pressure = 1 atm
- Time step used = 2 femtoseconds, Total Runtime=200 nanoseconds
GIF of the simulation(310K)
As we were expecting before, there is no gel phased lipids and interdigitation present in this case. To quantify the results, let us do the interdigitation analysis.
ANALYSIS
I did the same analysis for interdigitation as in the last time.
We see that the average interdigitation distance is more or less constant in the case of the heated system(310K). In the 290K system, the average interdigitation goes to negative which means there are significant interdigitation events happening in the lipids of upper and lower layer leaflets.
All files available at my GITHUB repository
LINKS :
- https://github.com/dexterdev/STEEMIT/tree/master/DMPC_290K/
- https://github.com/dexterdev/STEEMIT/tree/master/DMPC_310K/
References [Books for further reading]
Textbook references for learning theory of Molecular Dynamics:
- "Statistical Mechanics: Theory and Molecular Simulations" by Mark E. Tuckerman
- "Molecular Modelling: Principles and Applications" by Andrew R. Leach
- "Computer Simulation of Liquids" by D. J. Tildesley and M.P. Allen
Regarding Phospholipids and biophysics etc
- Physical Biology of Cell by Rob Philips et al.. [This is a great book.]
- From biological membranes to biomimetic model membranes
References specific to NAMD and VMD:
CHARMM-gui related papers:
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So is it a 2D or 3D simulation? I am guessing that everything is 3D because the molecular structure cannot be nicely embedded in 2D. Or is this wrong?
It is 3D simulation.
Is it possible to embed all the molecular dynamics in 2D?
What do you mean by embedding in 2d? Can you elaborate?
Is it possible to restrict the motion of the molecules to a flat surface?
It is technically possible. One 2D simulation which I can assume is graphene system. But I have not done anything similar.
Yes. you can simulate any hypothetical system in 2D.
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