[gmx-users] Slab shifts out of the simulation box

[Sohaib. Mohammed]

It is better to use CLAYff forcefield for your mineral surface and generate
the non-bonded parameters for solid-hydrocarbons interactions. You can use
CHARMM27 to generate the topology for your hydrocarbons.
Why did you use constraints only for h-bonds, how about all bonds.

Best,
Sohaib

On Tue, Sep 17, 2019 at 9:46 AM Mohammed Hamza <
mohammedhamzakhalaf at gmail.com> wrote:

> Dear GMX users
>
> I'm simulating a mixture of hydrocarbons on a slab of mineral using
> CHARMM27 ff. The topology of the slab was generated using the interface
> forcefield script.
> I see the slab shifts out of the simulation box (shown in the links below)
> and get "There were 724 inconsistent shifts. Check your topology".
> I check the topology and I don't see anything unusual.
> Any ideas what is going on?
>
> Thanks in advance
>
>
> https://www.dropbox.com/s/hppbfa7pse6htem/final%20slab.png?dl=0
> https://www.dropbox.com/s/hk3d0mrkew7c55s/initial%20box.png?dl=0
>
> Here is the mdp that I used
>
> ; Run parameters
> integrator     = md ; leap-frog integrator
> nsteps     = 50000        ; 2 * 25000000 = 50000 ps
> dt     = 0.001 ; 2 fs
> ; Output control
> nstxout = 500 ; save coordinates every 1.0 ps
> nstvout = 500 ; save velocities every 1.0 ps
> nstenergy = 500 ; save energies every 1.0 ps
> nstlog = 500 ; update log file every 1.0 ps
> nstxout-compressed = 500
> ; Bond parameters
> constraint_algorithm        = lincs    ; holonomic constraints
> constraints             = h-bonds
> 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    = 1.2 ; 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 = V-rescale        ; modified Berendsen thermostat
> tc-grps = System        ; two coupling groups - more accurate
> tau_t = 0.1                ; time constant, in ps
> ref_t = 350                ; reference temperature, one for each group, in
> K
>
> ; Periodic boundary conditions
> pbc     = xyz ; 3-D PBC
> periodic-molecules   = yes
> ; Dispersion correction
> DispCorr     = no
> ; Velocity generation
> gen_vel      = no ; Velocity generation is off
> --
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