[gmx-users] Membrane protein simulation isotropic vs semiisotropic

[Justin Lemkul]

On 6/15/19 8:56 AM, paul buscemi wrote:
> 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.

Applying surface tension and semiisotropic coupling will result in 
different ensembles. The former yields NPgammaT, the latter NPT. 
Semiisotropic pressure coupling is the de facto standard in modern 
membrane simulations unless an additional surface tension is necessary.

-Justin

> 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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-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
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