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

[Gmx QA]

Thanks Justin, those are good points.

A quick follow up, would you (or someone else) consider the APL-values I
have for my mixed bilayer system to be good, just ok-ish or plain wrong?

THANKS



2013/5/8 Justin Lemkul <jalemkul at vt.edu>

>
>
> 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
>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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