[gmx-users] Membrane protein simulation isotropic vs semiisotropic

[Prasanth G, Research Scholar]

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.