[gmx-users] Equilibration using position restraints in NPT

[Mark Abraham]

Hi,

The simplest explanation is that your box size is inappropriate for the
contents. If the box wants to change size but the nanotube is restrained to
fixed positions then you have an invalid model.

Mark

On Sun, 8 Oct 2017 15:39 Neha Gandhi <n.gandhiau at gmail.com> wrote:

> 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,
> --
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