[gmx-users] lipids per area charmm36 popc

[Justin A. Lemkul]

Peter C. Lai wrote:
> Hello
> 
> I am trying to equilibrate from scratch a 196 POPC bilayer using Tom's
> charmm36.ff. My box has a lot of TIPS3P (charmm) waters above and below 
> the membrane with a box size around 8.5x8.5x12.7. My desired end state 
> is to only use the setup for g_membed but I'd also like to get a pristine 
> tall bilayer that might be useful for other things or colleagues. I ran 
> 1ns NPT so far with:
> 
> dt              = 0.002
> 
> continuation    = yes            
> constraint_algorithm = lincs    
> constraints     = all-bonds     
> lincs_iter      = 1             
> lincs_order     = 4             
> ns_type         = grid          
> nstlist         = 5
> 
> rlist           = 1.2           
> rlistlong       = 1.4
> rcoulomb        = 1.2           
> rvdw            = 1.2          
> vdwtype         = switch
> rvdw_switch     = 0.8
> coulombtype     = PME            
> pme_order       = 4             
> fourierspacing  = 0.16          
> 
> tcoupl          = Nose-Hoover   
> tc-grps         = POPC SOL      
> tau_t           = 0.5   0.5     
> ref_t           = 300   300      
> pcoupl          = Parrinello-Rahman         
> pcoupltype      = semiisotropic
> tau_p           = 4
> ref_p           = 1.01325 1.01325
> compressibility = 4.5e-5 4.5e-5
> DispCorr        = no
> comm_mode       = Linear
> comm_grps       = POPC SOL
> 
> The metrics look roughly stable:
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> ---------------------------------------------------------------------
> Temperature                     300    0.00018   0.957697 0.000466096  (K)
> Density                     1017.26       0.24     1.5953     1.4803  (kg/m^3)
> Pressure                    1.00795      0.065    99.5783 -0.0431925  (bar)
> Box-X                       8.58491      0.036  0.0773839  -0.235388  (nm)
> Box-Y                       8.59611      0.036  0.0774849  -0.235696  (nm)
> Box-Z                       12.4357        0.1   0.216337   0.659896  (nm)
> 
> My APLs are ~10A^2/lipid above what they "should be" according to Klauda
> and experimental (I get 76-77A^2/lipid vs 65-58A^2/lipid). I suppose
> with TIPS3P water, I could get closer LJ packing if I turned on DispCorr
> but I thought that you generally left that off in charmm36 bilayer runs...
> 
> Now, I also could extend for several ns until density/box drift gets 
> smaller, but any other thoughts (yes this is probably a continuation of the 
> CHARMM36 lipid bilayers thread from October 
> (http://www.mail-archive.com/gmx-users@gromacs.org/msg34582.html)?

Later in this thread it is suggested that one use TIPS3P ("CHARMM TIP3P") water, 
so start there, although that discussion found that the APL was consistently 
underestimated, not overestimated, as is your case.

1 ns is not nearly enough to make solid conclusions about membranes.  Lipid 
rotational relaxation is on the order of 5 ns, and translational relaxation 
about 10 ns.  I'd say you need at least 20 ns of simulation to make any real 
conclusions, with some of that of course discarded as equilibration.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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