[gmx-users] membrane region fixed

[Mark Abraham]

Hi,

You're using quite an old version of GROMACS, which unfortunately means the
warning message issued by GROMACS 2018 and more recent is not available to
you (
http://manual.gromacs.org/documentation/2018/release-notes/miscellaneous.html#added-grompp-note-for-parrinello-rahman-position-restraints).
That suggests Berendsen pressure coupling in such cases, because position
restraints within a box whose volume changes is not an intrinsically well
defined model. Asking your compute center for a more recent GROMACS version
will probably run faster and have fewer bugs, too ;-)

Mark

On Tue, 18 Jun 2019 at 12:18, Patricia Saenz Méndez <sabioncita at gmail.com>
wrote:

> Hi!
> I am trying to run a simulation of a membrane protein (without the
> membrane), and to this end I am trying to fix the region of the protein
> that is inserted in the hydrophobic part of the membrane. It is not a
> transmembrane protein, just an helix is"touching" the lipophylic part of
> the membrane.
> I used genrestr and an index file. I could equilibrate the system. But when
> trying to run the actual MD simulation (200 ns) I just get the calculation
> finished in a couple of minutes and apparently just run 100 ps (like during
> equilibration).
> There it goes the command line (gromacs 5.1):
>
> mpirun -np 200 gmx_mpi grompp -f md_NPT_200ns.mdp -c 1w6j-wild_npt.gro -t
> 1w6j-wild_npt.cpt -p 1w6j-wild.top -n index.ndx -o 1w6j-wild_md_200ns.tpr
>
> mpirun -np 200 gmx_mpi mdrun -s 1w6j-wild_npt.tpr -deffnm
> 1w6j-wild_md_200ns
>
> and the mdp file:
>
> define      = -DPOSRES_MEMBRANE ; position restrain the membrane region
> ; Run parameters
> integrator  = md        ; leap-frog integrator
> nsteps      = 100000000  ; 2 * 100000000 = 200000 ps (200 ns)
> dt          = 0.002     ; 2 fs
> ; Output control
> nstxout             = 5000000         ; save coordinates every 100.0 ps
> nstvout             = 5000000         ; save coordinates every 100.0 ps
> nstenergy           = 2500            ; save energies every 5.0 ps
> nstlog              = 25000          ; update log file every 50.0 ps
> nstxtcout           = 2500           ; write .xtc trajectory every 5.0 ps
> energygrps          = Protein
> ; Bond parameters
> continuation    = yes           ; first dynamics run
> 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         = 5         ; 10 fs, largely irrelevant with Verlet
> 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
> tcoupl      = V-rescale                     ; modified Berendsen thermostat
> tc-grps     = Protein Non-Protein    ; two coupling groups - more accurate
> tau_t       = 0.1   0.1                     ; time constant, in ps
> ref_t       = 300   300                     ; reference temperature, one
> for each group, in K
> ; Pressure coupling
> pcoupl      = Parrinello-Rahman             ; pressure coupling is on for
> NPT
> pcoupltype  = isotropic                     ; uniform scaling of box
> vectors
> tau_p       = 2.0                           ; time constant, in ps
> ref_p       = 1.0                           ; reference pressure, in bar
> compressibility = 4.5e-5                    ; isothermal compressibility of
> water, 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        ; assign velocities from Maxwell distribution
>
>
> What am I doing wrong?
> Thanks in advance,
>
> P
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