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

[Mohammed Hamza]

Dear Sohaib

I did use all-bonds and was the same. I wonder why the slab shifts

Best Regards,
Mohammed

On Tue, Sep 17, 2019 at 10:08 AM Sohaib. Mohammed <
sohaibmohammed10 at gmail.com> wrote:

> 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
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>