[gmx-users] Protein-POPC bilayer

[Peter C. Lai]

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			|
==================================================================