[gmx-users] Protein-POPC bilayer
Shima Arasteh
shima_arasteh2001 at yahoo.com
Fri Aug 17 05:35:23 CEST 2012
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 |
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