[gmx-users] area per lipid

[Shima Arasteh]

I pick the snapshots every 10ns, because I don't know how much time this system needs to be simulated to reach to the proper APL.

The md.mdp dile I used here is:

title        = Production run for Water-POPC system

; Parameters describing the details of the NVT simulation protocol
integrator    = md        
dt        = 0.002            
nsteps        = 5000000    

; Parameters controlling output writing
nstxout        = 1000        
nstvout        = 1000        
nstenergy    = 1000        
nstlog        = 1000        

; Parameters describing neighbors searching and details about interaction calculations
ns_type        = grid    
nstlist        = 5        
rlist        = 1.2    
rcoulomb    = 1.2    
rvdw        = 1.2    
pbc        = xyz        

; Parameters for treating bonded interactions
continuation    = yes            
constraint_algorithm = LINCS    
constraints    = all-bonds            
lincs_iter    = 1                    
lincs_order    = 4                    

; Parameters for treating electrostatic interactions
coulombtype    = PME            
pme_order    = 4                
fourierspacing    = 0.16        

; Temperature coupling parameters
tcoupl        = Nose-Hoover    
tc-grps        = POPC SOL         
tau_t        = 0.5    0.5         
ref_t        = 300     300        

; Pressure coupling parameters
pcoupl        = Parrinello-Rahman        
pcoupltype    = semiisotropic            
tau_p        = 2.0                       
ref_p        = 1.0    1.0                  
compressibility = 4.5e-5    4.5e-5    


DispCorr    = EnerPres        
gen_vel        = no             
nstcomm        = 1            
comm_mode    = Linear    
comm_grps    =POPC SOL    



Sincerely,
Shima


________________________________
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Friday, November 9, 2012 12:20 AM
Subject: Re: [gmx-users] area per lipid



On 11/8/12 4:39 AM, Shima Arasteh wrote:
> Hi,
>
> I am trying to simulate POPC in water in 300 K, using charmm36 FF. In order to reach appropriate area per lipid ( 63-65 Angestroms per headgroup as mentioned in articles ), I let the system to be simulated for 40 seconds. To do so, I checked the area  per lipid every 10 ns. The results of area per lipid in each step are as below:
>
> 1.
> Top leaflet: 60.44
>
> Bottom leaflet: 59.43
>
>
> 2.
> Top leaflet: 61.135
> Bottom leaflet: 60.11
>
> 3.
> Top leaflet: 61.40
>
> Bottom leaflet: 60.38
>
> 4.
> Top leaflet: 60.27
>
> Bottom leaflet: 59.27
>
> I expected it to approaches the expected amount steadily, but why did I get such a result? How can I get to the appropriate area  per lipid?
>
> Would you please give me suggestions? Any suggestions would be appreciated.
>

Without seeing a complete .mdp file, it's hard to say.  Why are you picking 
snapshots every 10 ns?  You can easily plot APL over time for the entire 
trajectory using the box vectors stored in the .edr file from (Box-X * 
Box-Y)/(number of lipids).  You would have to write your own script to do the 
calculation, but it's quite straightforward.

-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

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