[gmx-users] Strange behaviour of added atomtype in simulation
m.kamps at student.rug.nl
Wed Nov 23 13:34:11 CET 2016
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.
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.
Any help would be great!
> 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
> <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
> 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)
> 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
> ; 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
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