[gmx-users] Protein-POPC bilayer

Shima Arasteh shima_arasteh2001 at yahoo.com
Fri Aug 17 06:04:35 CEST 2012



Oh, It's OK. Thanks Peter. :-)
I used the the same .mdp file sent me by you 1 month ago, for the pre-equilibration of POPC in water. 

But as others said here, anisotropic pressure coupling might result in major changes in lipid bilayer. I don't know, but it seems it is better to use anisotropic pressure coupling for the pre-equilibration of bilayer!? Right?! Anisotropic would be a better option? 

Now, I'd like to know which one is suggested to be used for the pre-equilibration before insertion of protein? Anisotropic is suggested?

Please make me clear here. Thanks for all explanations.


Sincerely,
Shima


----- Original Message -----
From: Peter C. Lai <pcl at uab.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>
Cc: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Friday, August 17, 2012 8:19 AM
Subject: Re: [gmx-users] Protein-POPC bilayer

Can't remember why I said that, since it's not what I used. Stupid 
autocorrect? Sorry!

On 2012-08-16 08:35:23PM -0700, Shima Arasteh wrote:
> In  "2.1.6. Membrane bilayer construction" part of the article you mentioned:
> 
> Asingle POPC molecule is parameterized using a
> CHARMM36 force field conversion for GROMACS7. The result-
> ing system,which consists of around 238 lipids is then equilibrated
> for at least 50 ns at 310 K and 1 atm under NPT ensemble with
> anisotropic pressure coupling or until the are a per lipid converges
> close to the consensus value of around 63–65Å per headgroup.
> 
> This is where I asked the question about.
> 
> Thanks.
> 
>  
> 
>  
> Sincerely,
> Shima
> 
> 
> ----- Original Message -----
> From: Peter C. Lai <pcl at uab.edu>
> To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
> Cc: 
> Sent: Friday, August 17, 2012 7:17 AM
> Subject: Re: [gmx-users] Protein-POPC bilayer
> 
> Here is my MDP file I use for POPC work for NPT-after-NVT equilibration, 
> in caes you lost it from the time before:
> You can choose to use V-rescale and Berendsen if you want but the Nose-Hoover/
> Parinello-Rahman with the paraeters below was stable for me with 238 POPC
> and 21524 water.
> 
> 
> integrator      = md            ; leap-frog integrator
> nsteps          = 2500000         ; 2 * 50000 = 100 ps
> dt              = 0.002         ; 2 fs
> ; Output control
> nstxout         = 1000           ; save coordinates every 0.2 ps
> nstvout         = 1000           ; save velocities every 0.2 ps
> nstenergy       = 100           ; save energies every 0.2 ps
> nstlog          = 100           ; update log file every 0.2 ps
> 
> continuation    = yes            ; NOT first dynamics run
> constraint_algorithm = lincs    ; holonomic constraints
> constraints     = h-bonds     ; all bonds (even heavy atom-H bonds) constrained
> lincs_iter      = 1             ; accuracy of LINCS
> lincs_order     = 4             ; also related to accuracy
> ; Neighborsearching
> ns_type         = grid          ; search neighboring grid cells
> nstlist         = 5             ; 10 fs
> rlist           = 1.2           ; short-range neighborlist cutoff (in nm)
> rlistlong       = 1.4
> rcoulomb        = 1.2           ; short-range electrostatic cutoff (in nm)
> rvdw            = 1.2           ; short-range van der Waals cutoff (in nm)
> vdwtype         = switch
> rvdw_switch     = 0.8
> ; Electrostatics
> coulombtype     = PME           ; Particle Mesh Ewald for long-range electrostatics
> pme_order       = 4             ; cubic interpolation
> fourierspacing  = 0.16          ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl          = Nose-Hoover     ; modified Berendsen thermostat
> tc-grps         = POPC SOL      ; two coupling groups - more accurate
> tau_t           = 0.5   0.5     ; time constant, in ps
> ref_t           = 300   300     ; reference temperature, one for each group, in K
> pcoupl          = Parrinello-Rahman            ; no pressure coupling in NVT
> pcoupltype      = semiisotropic
> tau_p           = 4
> ref_p           = 1.01325 1.01325
> compressibility = 4.5e-5 4.5e-5
> 
> ; Periodic boundary conditions
> pbc             = xyz           ; 3-D PBC
> ; Dispersion correction
> DispCorr        = no    ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel         = no           ; assign velocities from Maxwell distribution
> ;gen_temp        = 300           ; temperature for Maxwell distribution
> ;gen_seed        = -1            ; generate a random seed
> nstcomm         = 1
> comm_mode       = Linear
> comm_grps       = POPC SOL
> 
> On 2012-08-16 09:32:17PM -0500, Peter C. Lai wrote:
> > You always use semi-isotropic for bilayer work. The Z is decoupled from x-y 
> > due to symmetry.
> > 
> > I don't think I mention anything differently in the paper.
> > 
> > Pcoupltype               = semiisotropic
> > 
> > 
> > On 2012-08-16 04:26:38PM -0700, Shima Arasteh wrote:
> > > 
> > >  Hi,
> > > 
> > > I have a question about the Protein-POPC system:
> > > To insert a protein in lipid bilayer, I am suggested to simulate POPC in water separately before insertion, it might decrease the time of final simulation. It's OK!
> > > 
> > > In the article suggested me by dear Peter C. Lai, I read that POPC was simulated in anisotropic pressure coupling at first and then after insertion of protein, semi-isotropic pressure coupling is applied. 
> > > Now, would you please telling me why you used this procedure?
> > > And,
> > > Would my system be correct  if I use semi-isotropic pressure coupling instead of anisotropic pressure coupling for the first step?
> > > 
> > > Thanks in advance for your replies.
> > > 
> > > 
> > > Sincerely,
> > > Shima
> > > -- 
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> > ==================================================================
> > Peter C. Lai            | University of Alabama-Birmingham
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> ==================================================================
> Peter C. Lai            | University of Alabama-Birmingham
> Programmer/Analyst        | KAUL 752A
> Genetics, Div. of Research    | 705 South 20th Street
> pcl at uab.edu            | Birmingham AL 35294-4461
> (205) 690-0808            |
> ==================================================================

-- 
==================================================================
Peter C. Lai            | University of Alabama-Birmingham
Programmer/Analyst        | KAUL 752A
Genetics, Div. of Research    | 705 South 20th Street
pcl at uab.edu            | Birmingham AL 35294-4461
(205) 690-0808            |
==================================================================



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