[gmx-users] Strange behaviour of added atomtype in simulation

[Kamps, M.]

Dear gmx-users,

Is there anybody that can say anything about my simulation as to why
it would fail?
To clarify I've added some images. The first image is taken at t=0,
right after the equilibration steps, while the second image is taken
after around 0.08ns of simulations. This simulation was done in water,
however the same happens in vacuum.
https://postimg.org/image/7byeyjxo5/
https://postimg.org/image/6nfjwndyb/
As you can see, the relative order in the first image has completely
disappeared, atoms have left the FCC structure and the atoms behave
like a liquid. Atoms are also leaving the plane, and move through the
upper or lower PBC to rejoin the surface at the other side. Again,
this behaviour only happens at T=300K but not at T=10K. I understand
that atoms behave different at lower temperatures, however this
behaviour should not happen at these temperatures?
I've uploaded my files, so if you are interested you can take a look.
The first link contains all files and all simulation results, while
the second link contains only the files.
https://ufile.io/5f217
https://ufile.io/d3622
Any help would be great!

Mark

> Message: 6
> Date: Mon, 21 Nov 2016 21:05:02 +0100
> From: "Kamps, M." <m.kamps at student.rug.nl>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Strange behaviour of added atomtype in simulation
> Message-ID:
>         <CACsKKu3iNNz2S=MgbOFQd4mzjndmuASweRjMDJ1hMqmAGLDvdw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear gmx-user.
>
> I am trying to implement an an-organic ionic-bound surface into GROMACS.
> I've added the residue (which is Al, aluminium, uncharged) into an rtp
> file, and added this to an edited Charmm force-field. The atom is added to
> atomtypes.atp and ffnonbonded.itp. The LJ potentials are found from the
> literature.
> The surface is created by insert-molecules the individual atoms in a
> specific FCC orientation. I then simulated the surface in a vacuum to see
> how it behaves. To enable this, the surface is energy minimized and NVT and
> NPT equilibriated.
>
> The problem arises when it is simulated at room temperature (300K), where
> the surface will behave like a liquid, instead of a solid. This seems
> strange since the critical temperature is not reached by far. I tried
> testing the surface at a lower temperature (10K) and there it behaves as
> expected. At 10K the surface will stay in shape, in its optimal FCC
> configuration and it will slightly vibrate as expected.
> If the temperature is set to 300K, the surface will immediately deform and
> atoms will move all through each other and around each other. The surface
> will keep its shape, due to atomistic interactions, however it will not
> stay in its optimal FCC configuration, which is what should happen.
>
> What am I doing wrong?
>
> The used md.mdp file is given below:
> title = Al Surface MD simulation
> ; Run parameters
> integrator = md-vv ; leap-frog integrator
> nsteps = 200000 ; 1 * 200000 = 200 ps (0.2 ns)
> dt     = 0.001 ; 1 fs
> ; Output control
> nstxout       = 1000 ; save coordinates every 1.0 ps
> nstvout         = 1000 ; save velocities every 1.0 ps
> nstenergy         = 1000 ; save energies every 1.0 ps
> nstlog         = 1000 ; update log file every 1.0 ps
> ; Bond parameters
> continuation       = yes ; Do not continue
> 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     = cut-off ; Particle Mesh Ewald for long-range
> electrostatics
> ; Temperature coupling is on
> tcoupl = berendsen        ; modified Berendsen thermostat
> tc-grps = AL ; one coupling group
> tau_t = 0.1          ; time constant, in ps
> ref_t = 300          ; reference temperature, one for each group, in K
> ; Pressure coupling is on
> pcoupl       = berendsen ; Pressure coupling on in NPT
> pcoupltype         = semiisotropic        ; scaling with different value in
> z direction
> tau_p         = 2.0        ; time constant, in ps
> ref_p         = 0.0 0.0        ; reference pressure, for both directions,
> in bar
> compressibility     = 0.0 4.5e-5        ; compressibility, for both
> directions, in bar^-1 (4.5e-5)
> ; Periodic boundary conditions
> pbc = xyz ; 3-D PBC
> ; Velocity generation
> gen_vel = no ; velocity generation is off
> ; Dispersion correction
> DispCorr = EnerPres ; account for cut-off vdW scheme
>
> ******************************************************