[gmx-users] lipids per area charmm36 popc

[Peter C. Lai]

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)?


Thanks
-- 
===============================================================
Peter C. Lai                 | University of Alabama-Birmingham
Programmer/Analyst           | BEC 257
Genetics, Div. of Research   | 1150 10th Avenue South
pcl at uab.edu                  | Birmingham AL 35294-4461
(205) 690-0808               |
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