GROMOS53a6 Gromacs by XYZ

The package viewer shows the meta data for the package and the available versions, i.e. the history of the parameters. Note that files can differ between versions, in which case the SHA1 checksum after the filename will differ. You can read and add comments for a particular version through the View discussion button on each version.

If you are the curator of a package (i.e. you added it) and you are logged in then you can also edit the package.

Lipid 1,2-diphytanoyl-sn-glycero-3-phosphocholine (DPhyPC)
Pubchem CID:169428
Forcefield GROMOS53a6
Code Gromacs
Authors D'Rozario R
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Robert D'Rozario

Please check the stereochemistry of the glycerol backbone before simulating! Check the R/S configuration. If it's the correct one you want then go ahead and simulate!

I created the bilayer by setting up an 8x8 DPhPC leaflet then copy and rotate by 180 deg to get your bottom layer (all done with a bit of editconf!). You then have a more or less regular looking bilayer- add water, ~40 waters per lipid molecule to the box (solvating the tails of the lipid aswell) then simulated for 10 ns.


D'Rozario R, (2009), [no doi], [no pubmed id] Notes: (unpublished)
Primary Experimental


Version 1
DPHPC.itp e2d9fb697898ea4a69cd26f63a191d6098b9a483
ffG53a6bonrob.itp 36493d8950b1c75ca0426acd1e5863a04b1382d8
ffG53a6nbrob.itp 4348ee99fdc3e56c2c0ea8ecb7b0e1498ccc53c5
ffG53a6rob.itp 94edd1010f2dee31d67b898d7516a7ca73d8f5bc
PDB structure
1-DPhPC.pdb d9de39e5ea3dbffa0b1849b5897f01fa0ddcd89a
Bilayer structure
md.gro 1c85b1336111b58c668f938bca4811b41e56d0c1