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

[Prasanth G, Research Scholar]

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.