use GAFF parameters by Lula Rosso with an applied surface tension (available on the Bryce website) If you want to run DMPC at the experimental area per lipid using amber the following options are open to you: This affected the gafflipid work and mean the lipid parameters require more attention.Īs a consequence running a DMPC with gafflipid causes the area per lipid to drop to about 56A^2, which is below the experimental 60A^2 though the bilayer is still liquid phase. These were a particular issue when using the GPU code.
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We have had a number of issues with bilayer simulations in amber related to the rapid collapse of the simulation box in the initial stages of simulation. On Wed, at 1:37 PM, Dickson, Callum > wrote: I hope this will be fixed in next coming amber force filed (Lipid 12). The area per lipid is going even less than 56 A^2 and bilayer getting freeze.I got 49 A^2 after 50 ns. I tested the GAFFLipid force field extensively on CPUs. So I think the issue is more one of simulation protocol here than the GAFF Lipid parameters. Subject: Re: Fwd: DMPC GAFF lipid membrane is freezing at 303 K.Ĭallum, can you show Subbarao how you are getting DMPC at 56A^2 - I believe the 50A^2 being seen here is an issue with protocol - essentially if you are too aggressive you can freeze your bilayer and then it will take a LONG (read 10s of microseconds) to 'unfreeze'. I will send these input files, prmtop, coordinates etc off list so you can test for yourself.įrom: Ross Walker # 10x 500ps NPT sequential restarts using the following input to collapse simulation box
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CPU and GPU code should give comparative results. I ran a 128 DMPC bilayer using gafflipid parameters out to about 30ns on a GPU and it remained stable at 56A^2.