[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
> > 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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> ==================================================================
> 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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