Please, could someone help me with that ? Are my questions unclear ? 2016-12-09 9:48 GMT+01:00 Sim gmx <sim...@gmail.com>:
> Hello everyone, > > I am currently working on interactions between small biomolecules and > bilayers. Phospholipids parameters come from Peter Tieleman's website > (Berger lipids forcefield) and the small compounds are parametrized for > gromos53a6. I would like to add cholesterol to my bilayers, which is very > frequently done with Höltje cholesterol parameters (see e.g. > http://pubs.acs.org/doi/full/10.1021/ja211929h ). However, these Höltje > parameters were originally designed for the ffgmx forcefield, which is > quite old. > > The way we should include these parameters in a Berger lipids - gromos53a6 > mixed forcefield has already raised some questions on the mailing list: > http://comments.gmane.org/gmane.science.biology.gromacs.user/68478 > > However, it remains unclear to me. I guess we can use the bonded > parameters as they are written in the original topology from Höltje, but it > becomes more complicated when talking about the non bonded interactions. > Every atomtypes but two (CB and CR61) from ffgmx also exist in gromos53a6 > (and are thus included in the gromos53a6 forcefield). Hence, I think there > are 3 possible ways to make a simulation run without crashing when > including this cholesterol to a berger lipid - gromos53a6 forcefield: > > 1) Keeping the cholesterol topology file unchanged, and adding the > atomtypes 'CB' and 'CR61' to the forcefield file 'ffnonbonded.itp', with > their parameters coming from the ffgmx forcefield. It means that each > cholesterol will be seen as a "hybrid object", with most of the atomtypes > being gromos53a6 ones, and CB and CR61 being ffgmx atomtypes. Non bonded > interaction involving CB or CR61 atomtypes will be computed with the > standard combination rule. > > 2) Keeping the Berger lipid - gromos53a6 forcefield unchanged, and > changing the atomtype 'CB' to 'C' and the atomtype 'CR61' to 'CR1' into the > cholesterol topology file, C and CR1 being the corresponding atomtypes > found in gromos53a6. It means that each cholesterol will be seen as a > "gromos53a6" object for the non bonded interactions. > > 3) Changing every atomtype from the cholesterol topology file to make them > different from gromos53a6 atomtypes (for instance: CH2 becomes CH2F (for > ffgmx)) and adding all these ffgmx specific atomtypes in the forcefield > file 'ffnonbonded.itp' with the proper parameters. It means that each > cholesterol will be seen as a "ffgmx object", each non bonded interaction > being computed with the standard combination rule. > > Solution 1 seems to be quite obvious, but it sounds a bit weird to me, > because it mixes up ffgmx and 53a6 interactions. Solution 2 seems more > consistent, but if we use "pure" gromos53a6 non bonded interactions, maybe > we should also "translate" bonded parameters from ffgmx to gromos53a6 ? > Solution 3 is maybe the most logical solution, but it seems that ffgmx is > now considered to be deprecated... > > The question becomes even more complicated when considering the fact that > CH2 and CH3 atomtypes could lead to overcondensed bilayers, according to > some authors who advise to switch them to 'LP2' and 'LP3' Berger lipid > atomtypes. > > It is possible that those solutions give quite similar results (if ffgmx > and gromos53a6 forcefields are "similar enough"), but I am very curious to > know the 'usual' protocol that is followed when people only write "Höltje > parameters were used". > > Another solution would be to use the cholesterol topology file found on > ATB (manual validation), frequently used by Pr. Alan E. Mark, but never > used with Berger lipids phospholipids... > > Thank you in advance for your help! > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.