[gmx-users] Equilibration using position restraints in NPT

[Neha Gandhi]

This is a very common post on previous mailing list however, I am still not
able to fix the problem of position restraints during NPT.

I have a carbon nanotube aligned to z-direction. I am trying to simulate
infinite nanotube using periodic conditions. It is common to use position
restraints for nanotube (most papers report this). I have imposed position
restraints on nanotube and in doing so, the coordinates fluctuates by 0.5-1
nm. This is not an issue with NVT simulation (Berendsen thermostat and
barostat). I tried different thermostats and barostats, they deform the
nanotube as previously discussed on gromacs mailing list.

How do I equilibrate nanotube system with position restraints when used
together with pressure coupling? Should I play with the box size after
first NVT run?
The force field is opls based on gromacs guideline on CNTs and GROMACS
version is 5.1.4. The mdp parameters are below:

Thank you in advance,

Sincerely,
Neha



title        = OPLS Lysozyme NPT equilibration
define        = -DPOSRES_CNT    ; position restrain the protein
; Run parameters
integrator    = md        ; leap-frog integrator
nsteps        = 500000        ; 2
dt            = 0.001        ; 2 fs
; Output control
nstxout        = 5000        ; save coordinates every 1.0 ps
nstvout        = 5000        ; save velocities every 1.0 ps
nstenergy    = 5000        ; save energies every 1.0 ps
nstlog        = 5000        ; update log file every 1.0 ps
;energygrps               = Protein  CNT Water NA
; Bond parameters
continuation            = yes        ; Restarting after NVT
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
cutoff-scheme   = Verlet
ns_type            = grid        ; search neighboring grid cells
nstlist            = 10        ; 20 fs, largely irrelevant with Verlet
scheme
rcoulomb        = 1.0        ; short-range electrostatic cutoff (in nm)
rvdw            = 1.0        ; 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        = Berendsen                    ; modified Berendsen thermostat
tc-grps        = CNT Water    ; two coupling groups - more accurate
tau_t        = 0.2      0.2            ; time constant, in ps
ref_t        = 310       310           ; reference temperature, one for
each group, in K
; Pressure coupling is on
pcoupl                = Berendsen        ; Pressure coupling on in NPT
pcoupltype            = isotropic                ; uniform scaling of box
vectors
tau_p                = 5.0                    ; time constant, in ps
ref_p                = 1.0                    ; reference pressure, in bar
compressibility     = 4.5e-5                ; isothermal compressibility of
water, bar^-1
refcoord_scaling    = com
; Periodic boundary conditions
pbc        = xyz        ; 3-D PBC
periodic_molecules = yes
; Dispersion correction
DispCorr    = EnerPres    ; account for cut-off vdW scheme
; Velocity generation
gen_vel        = no        ; Velocity generation is off

-- 
Regards,
Dr. Neha S. Gandhi,