[gmx-users] Protein-POPC bilayer

Shima Arasteh shima_arasteh2001 at yahoo.com
Fri Aug 17 06:22:15 CEST 2012 


 :-)
  Thanks Peter.


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 8:48 AM
Subject: Re: [gmx-users] Protein-POPC bilayer

On 2012-08-16 09:04:35PM -0700, Shima Arasteh wrote:
> 
> 
> 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. 
> 

Well if that worked out, then what is the problem?

What do you mean by "pre-equlibration" The only step that happens before
equilibraiton is energy minimzation... If NPT is crashing after EM then
try a few ns of NVT (with a V-rescale thermostat) first, but because VMD
gives you highly ordered bilayer (straight chains), I believe I was able
to go from EM directly to NPT without any problems.

> 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.

You are welcome to try using anisotropic pressure coupling. With a system of
the size I put forth, it could be large enough[1] to "buffer" against box 
shearing forces.

[1] Anezo et. al J. Phys. Chem. B 2003, 107, 9424-9433

If you already equilibrated the membrane before insertion then go ahead and 
do the insertion. As was stated before, if the box vectors and area per lipid
are in equilibrium by the end of the equilibration, you should be fine.

> 

> 
> 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
> > > Programmer/Analyst        | KAUL 752A
> > > Genetics, Div. of Research    | 705 South 20th Street
> > > pcl at uab.edu            | Birmingham AL 35294-4461
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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            |
> ==================================================================

-- 
==================================================================
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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