[gmx-users] Membrane protein simulation isotropic vs semiisotropic

[paul buscemi]

The pressure on a (real-life)  membrane is not isotropic, edges are under tension. so using the p-couple “surface-tension”  - with water layers is appropriate. 

If you use p-couple  = isotropic  you should end up with a micelle because the hydrophobic effects are significant.


p

> On Jun 14, 2019, at 11:18 PM, Prasanth G, Research Scholar <prasanthghanta at sssihl.edu.in> wrote:
> 
> Dear Bratin,
> 
> When I am using a semiisotropic condition the pbc box is
> deforming/compressing pushing the lipid bilayer apart. I am attaching the
> screenshots of the system at the beginning(normal.png) of production run as
> well as at the end of 30ns simulation (elongated.png) for your reference.
> 
> This was my production mdp (md.mdp) file:
> ----
> title       = pro-DPP-LIG  Production MD
> ; Run parameters
> integrator  = md        ; leap-frog integrator
> nsteps      = 15000000    ; 2 * 15000000 = 30000 ps (1 ns)
> dt          = 0.002     ; 2 fs
> ; Output control
> nstxout     = 1000      ; save coordinates every 2 ps
> nstvout     = 1000      ; save velocities every 2 ps
> nstxtcout   = 1000      ; xtc compressed trajectory output every 2 ps
> nstenergy   = 1000      ; save energies every 2 ps
> nstlog      = 1000      ; update log file every 2 ps
> ; Bond parameters
> continuation            = yes       ; Restarting after NPT
> constraint_algorithm    = lincs     ; holonomic constraints
> constraints             = all-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 cels
> nstlist     = 5         ; 10 fs
> rlist       = 1.2       ; short-range neighborlist cutoff (in nm)
> rcoulomb    = 1.2       ; short-range electrostatic cutoff (in nm)
> rvdw        = 1.2       ; short-range van der Waals cutoff (in nm)
> ; 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                   ; More accurate thermostat
> tc-grps     = Protein_LIG_DPP   Water_and_ions  ;
> tau_t       = 0.5           0.5             ; time constant, in ps
> ref_t       = 323           323             ; reference temperature, one
> for each group, in K
> ; Pressure coupling is on
> pcoupl      = Parrinello-Rahman     ; Pressure coupling on in NPT
> pcoupltype  = semiisotropic         ; uniform scaling of x-y box vectors,
> independent z
> tau_p       = 2.0                   ; time constant, in ps
> ref_p       = 1.0   1.0             ; reference pressure, x-y, z (in bar)
> compressibility = 4.5e-5    4.5e-5  ; isothermal compressibility, bar^-1
> ; Periodic boundary conditions
> pbc         = xyz       ; 3-D PBC
> ; Dispersion correction
> DispCorr    = EnerPres  ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel     = no        ; Velocity generation is off
> ; COM motion removal
> ; These options remove motion of the protein/bilayer relative to the
> solvent/ions
> nstcomm         = 1
> comm-mode       = Linear
> comm-grps       = Protein_LIG_DPP  Water_and_ions
> ---
> *LIG is ligand and
> DPP is DPPC.
> 
> Thank you.
> 
> normal.png
> <https://drive.google.com/a/sssihl.edu.in/file/d/1BLR5UG8jwWnwnS4wmt1W-qIks4YCijPp/view?usp=drive_web>
> 
> elongated.png
> <https://drive.google.com/a/sssihl.edu.in/file/d/14yDNhlBJKbhhgFdpIYtr7SGhQIMoJrq6/view?usp=drive_web>
> 
> On Fri, Jun 14, 2019 at 12:09 PM Prasanth G, Research Scholar <
> prasanthghanta at sssihl.edu.in> wrote:
> 
>> Dear all,
>> 
>> Can someone please tell me if it is okay to use isotropic pcoupltype for a
>> membrane protein simulation? Are there any disadvantages?
>> 
>> Also, why is semiisotropic preferred over isotropic, in membrane protein
>> simulations..
>> 
>> Thank you.
>> --
>> Regards,
>> Prasanth.
>> 
> 
> 
> -- 
> Regards,
> Prasanth.
> -- 
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