[gmx-users] mdp-settings for charmm36 and lipid apl values

[Justin Lemkul]

On 5/8/13 11:09 AM, Gmx QA wrote:
> Hi gmx-users,
>
> I've been experimenting with simulations of mixed bilayers (512 lipids in
> total, 70% POPC, 30% POPE) using the charmm36 parameter set in gromacs, and
> have a couple of questions. I know this has been discussed before, but I'd
> appreciate some input nonetheless :-)
>
> The relevant sections of my mdp-file are pasted below:
>
> ; Start time and timestep in ps
> tinit                    = 0
> dt                       = 0.001
> nsteps                   = 100000000
>
> ; NEIGHBORSEARCHING PARAMETERS
> ; nblist update frequency
> nstlist                  = 5
> ; ns algorithm (simple or grid)
> ns_type                  = grid
> ; Periodic boundary conditions: xyz, no, xy
> pbc                      = xyz
> periodic_molecules       = no
> ; nblist cut-off
> rlist                    = 1.2
> ; long-range cut-off for switched potentials
> rlistlong                = 1.4
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype              = PME
> rcoulomb-switch          = 0
> rcoulomb                 = 1.2
> ; Relative dielectric constant for the medium and the reaction field
> epsilon_r                = 1
> epsilon_rf               = 1
> ; Method for doing Van der Waals
> vdw-type                 = switch
> ; cut-off lengths
> rvdw-switch              = 0.8
> rvdw                     = 1.2
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr                 = No
>
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> ; Temperature coupling
> tcoupl                   = V-rescale
> nsttcouple               = -1
> nh-chain-length          = 10
> ; Groups to couple separately
> tc-grps                  = System
> ; Time constant (ps) and reference temperature (K)
> tau_t                    = 0.1
> ref_t                    = 300
> ; Pressure coupling
> pcoupl                   = Parrinello-Rahman
> pcoupltype               = semiisotropic
> nstpcouple               = -1
>
> This is as far as I can tell from earlier discussions on the list, and also
> from reading the Piggott et al. paper in JCTC, the correct settings for
> charmm36.
>
> After a simulation of ~50 ns, I use GridMatMD to calculate the area per
> headgroup of POPC and POPE, respectively, and get what I think are not 100%
> acceptable results (but maybe they are)
>
> For POPC, I get 59,7 A^2, and for POPE, I get 63,1 A^2.
>
> The value for POPE would have been fine I suppose if it hadn't been for the
> fact that the APL for POPC is smaller. Should it not be larger than POPE?
>
> I notice in the Piggott-paper that they in the supplement for some
> simulations of POPC also get APL's of around 59-60 (without POPE of
> course), and that the results depend to some extent also on the usage of
> TIP3P vs TIP3SP water models. I have been using "normal" TIP3P here.
>
> Could anyone comment on (a) my mdp-file settings, and (b) the resulting
> APL, and tell me if I should be worried about anything?
>

The .mdp settings are fine as far as I can tell.  If you're concerned about 
accuracy, you should be analyzing a known system and trying to reproduce it. 
There is no reason in my mind why a binary lipid system should produce the 
behavior of a pure lipid system.  Lipids affect each other (just like all 
molecules do).  Headgroup interactions and acyl chain packing get more complex 
with increasing numbers of different lipids.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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