Markus Miettinen gave a talk and Samuli Ollila presented a poster describing the nmrlipids project. The presentations can be found below. If you have any questions or comments about the presentations you are welcome to comment this post. You can do this whether you were present in the meeting or not.
Talk (slides with no audio) presented by Markus Miettinen.
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| Poster presented by Samuli Ollila. |
Hi,
ReplyDeleteI did some simulations for POPC at 283 K using charmm36 with gromacs. I did it with the parameters provided in the McKerell site http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs and the bilayer goes straight to the gel phase, something that shouldn't happen. The box size keeps getting smaller and smaller even after 100ns.
Hi and welcome,
DeleteI have ran POPC with Charmm36 only in 303K. I also accidentally ran DPPC in 303K with Charmm36 and it did go to the gel phase, however this is what should happen. DPPC in 323K was liquid with Charmm36. I did start a POPC simulation with Charmm36 in 283K to see if I can reproduce your finding. I will let you know what happens.
I have now ran 10ns with CHARMM36 POPC at 283K. I do not see any signs of going to the gel phase. It would be nice to know what is the difference between our systems. You can find the mdp file I used here:
Deletehttps://www.dropbox.com/s/al9z6u3sjd5lkja/charmmT283.mdp?dl=0
and the force field parameters from here:
http://nmrlipids.blogspot.com/2013/10/welcome-if-you-are-new-here-reading.html?showComment=1382431179218#c1094382699388356948
Hi,
ReplyDeleteWe've run 100 ns using the charmm program and we do not see gel phase neither. When we saw the gel phase was because we used the mdp suggested in the slipids website (and to our knowledge slipids is an enhancement of the charmm parameters for lipids).
The parameters we used with the charmm program are the suggested in the charmm-gui website.
Thank your helpful comments.
Fernando.