[gmx-users] compressed pbc box at the end of simulation - membrane protein with ligand

[Bratin Kumar Das]

Hi
   This is happening because in ... pressure coupling you mentioned
semi-isotropic ...where the pressure will be uniform in x-y box vector..not
the z direction... that's why your box is becoming rectangular. You can use
isotropic pressure coupling for maintaining the sqare shape of the
box...generally the membrane simulation x=y is not equals to z.

On Tue 11 Jun, 2019, 10:19 AM Prasanth G, Research Scholar, <
prasanthghanta at sssihl.edu.in> wrote:

> Dear all,
>
> I am carrying out a simulation of membrane protein with a ligand. I am
> using DPPC [slipids (http://www.fos.su.se/~sasha/SLipids/Downloads.html)].
>
> I had modified amber 03 ff by including the non-bonded and bonded
> parameters from slipids website as suggested in the tutorial by Justin (
> http://www.mdtutorials.com/gmx/membrane_protein/).
>
> I had monitored NVT and NPT stages and as things were okay. I had proceeded
> with the production stage. However, at the end of 30ns simulation, I
> observe that the box gets compressed from a square to a highly compressed
> elongated rectangle (when viewed using both Chimera and VMD).
>
> Here is the md.mdp (for production run).
> ----
> title       = 4yl3-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.
>
> I request you to help me understand why this is happening and how i can
> overcome this.
> Thank you in advance.
>
> --
> Regards,
> Prasanth.
> --
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