Exercise 2: Car-Parrinello MD

In this chapter we will see some examples on how to setup a Car-Parrinello Molecular Dynamics run.

Hydrogen Molecule

Requirements: Memory: 50-100 MB, CPU time: 30-45 min.

For our first real Car-Parrinello MD simulations we start again small and simple: with the hydrogen molecule. For the following MD calculations you can re-use the RESTART.1 file from the previous calculation, or create a new one from the file 1-h2-wave.inp.

  1. From the previously optimized electron structure, we start some MD calculations for different timesteps (6a-h2-md-5au.inp, 6b-h2-md-4au.inp, 6c-h2-md-3au.inp). Since the pre-optimized wavefunction is done for an optimized geometry, we have to add some kinetic energy to the system to ‘see some action’. This is done via the keyword:

    TEMPERATURE 50.0d0
    Note that TEMPERATURE does not ‘control’ the temperature in any way, but only sets the initial kinetic energy of the system. Since we started from an optimized geometry, the average temperature during the simulation will be significantly lower.

    Please save the files ENERGIES and TRAJEC.xyz from each of those runs and compare them later using the appropriate visualization programs. What is the effect of the different time steps?
  2. If you don’t use a pre-calculated RESTART file, CPMD will still start the MD, but from an initial guess, which is usually far from the mininum, so that the MD will not be very meaningful and usually diverge after a few steps. If we disallow the atoms to move, and gradually remove kinetic energy (= annealing) from the electronic system, we can use the MD to optimize the the wavefunction (4f-h2-wave.inp).
         ANNEALING ELECTRON 0.98  
    will thus scale the velocities of the electronic degrees of freedom in each step with the factor of 0.98. Since annealing approaches the minimum via an exponential decay, it is quite efficient at the beginning, but rather inefficient to get to the fully optimized value.
  3. One can also use annealing of the kinetic energy for the atoms simultaneously to do a combined wavefunction and geometry optimization (7-h2-md-4au-ann.inp). Please note, that this procedure is rarely used and most useful when stopped early and followed by a normal geometry optimization.
  4. If a Car-Parrinello MD is not stable, i.e. the electronic degrees of freedom couple to the atom movements, one can increase the stability by increasing the fictitious mass of the electrons (8-h2-md-5au-emass.inp). This will however also impact the accuracy of the simulation. Please compare the resulting energies of this trajectory to the previous MD runs with the default fictitious mass of 400a.u. How does the higher electron mass affect the energies?
  5. Finally, one can also do a Born-Oppenheimer MD simulation with CPMD. Here in each step the wavefunction is fully re-optimized to the ground state (the BO-surface) (9-h2-bomd-20au.inp). Since the highest frequency determines the maximal length of the time step, with a BO-MD a (much) larger time step can be used. There is no (fictitious) dynamic of the electrons like in the CP MD, where the movement of the electrons (although significantly slowed down through the fictitious mass) still is much faster than atomic movements. How do both methods compare in terms of total efficiency (i.e. how much CPU time is needed to simulate a finite amount of time)? Note, that there are some ways to improve the efficiency of BO-MD calculations, that are currently not implemented in CPMD, so the comparison here is not entirely fair.

Ammonia Molecule in Gas Phase

As a next example we start an MD with ultra-soft pseudopotentials, starting from the restart of the optimized pyramidal (1-nh3-geoopt-vdb.inp) configuration.

  1. First we try to bring the system (roughly) into an equilibrium at 700K. This is most efficiently done by initializing the kinetic energy and then rescaling the velocities of the atoms whenever the instantaneous temperature is more than 50 Kelvin away from the target temperature of 700K. This is done by using (5-nh3-md-vdb.inp):

    Notice how the ‘potential energy’ (=EKS) increases at the beginning until it oscillates around an equilibrium.
  2. Now we want to continue without thermostatting, so those four lines are removed. But we want to continue the trajectory uninterrupted, so we have to read the in the velocities (for the electronic degrees of freedom as well as for the atoms). We do not rename the RESTART.1 file, but have CPMD directly restart from the last restart via the LATEST keyword. But you should rename the TRAJEC.xyz and the ENERGIES file, so that we have seperate files for both parts of the trajectory (if you don’t they will get appended, so you would have to cut them in parts later). When visualizing the trajectory, you may have notice, that the molecule translates and rotates. This is not ideal for an isolated molecule, but due to the intial starting conditions and numerical errors, those (unphysical) translational and rotational movement will always be there, and through the temperature control with rescaling they usually get emphasized as well. Since we want to look at an isolated molecule, we therefore redistribute the energy from those degrees of freedom to the rest by using the keyword SUBTRACT. Alltogether after removing the lines from above, we have to add the following lines (6-nh3-md-cont.inp):


Glycine Molecule

In Gas Phase

Requirements: Memory: 100 MB, CPU time: 10+30 min, equilibration, >6h h production.

By now we should be ready to create a first CPMD input file (almost) from scratch. We want to do an CP-MD simulation of an isolated glycine molecule. You can use the coordinates from the file gly.xyz and use the Ammonia molecule input as a template. Check out the CPMD manual for the supercell size requirements for the TUCKERMAN Poisson solver.

  1. Best you start with a wavefunction optimization with a very tiny cutoff (5 ry) and MAXSTEP set to 1. This is the fastest way to debug your input file (the wavefunction of that run is useless). Also compare the resulting GEOMETRY.xyz file with the example coordinates and see if the geometry is read correctly. Keep in mind, that SYMMETRY 0 implies centering of the molecule in the supercell.
  2. Now modify the &CPMD and &SYSTEM sections of your input file to be able to do a geometry optimization, using the proper plane wave cutoff. This is usually a good idea if you don’t have an equilibrium geometry to start from or are using coordinates from a molecule editor program. This way you make sure, that you don’t have too much potential energy in your system and it won’t ‘explode’ (Hint: 1-gly-opt.inp).
  3. Now start a CP MD simulation using the wavefunction and coordinates from the previous calculation and equilibrate the molecule for 500 steps to 300K via velocity rescaling. Please rename the ENERGIES, TRAJECTORY, TRAJEC.xyz files so that the following run does not append to them. Alternatively run them in different directories (Hint:2-gly-md-equilib.inp)
  4. Now turn off the velocity rescaling to continue with a production run without any temperature control (microcanonical ensemble) for (at least) 2000 steps. Note that you now have to read the velocities from the restart as well. Also you should only record every 10th step of the trajectory (using TRAJECTORY SAMPLE), so you don’t get a too large file (the time step is rather small so you would not see much difference between the individual configurations anyways) (Hint: 3-gly-md-cont.inp).
  5. Please, test also the feature of keeping a bookmark of several restart files, by adding the following lines:

    to the &CPMD section. This will write a restart file every 500 steps and name them alternating RESTART.1, RESTART.2, RESTART.3, and RESTART.4. Thus you won’t lose too much of your calculation if the job gets terminated for some reason in the middle of the trajectory. Using multiple restarts provides extra security in case there is file system corruption or the simulation starts behaving erratically at some point. CPMD simulations usually need a lot of computational effort, so it is good practice to avoid having to redo too much of a simulation in any case.

Monitor the various energies during the run. How do they correspond to the movement of the atoms?

Employing Thermostats

Requirements: Memory: 250 MB, CPU time: up to a few days..

For longer production MD simulations one usually couples the system to a heat bath via a thermostat algorithm. This is primarily done to compensate for small drift in the total energy due to numerical inaccuracies that accumulate slowly over the course of the simulation. Also the canonical NVT ensemble is usually more suited for calculation of thermodynamic properties than the microcanonical NVE ensemble.

For a simulation of a molecule in the gas phase the use of the MASSIVE thermostat is strongly recommended. In this context, massive does not refer to a more ‘strict’ or ‘powerful’ thermostat, but to a separate thermostat chain for each degree of freedom, i.e. massive referes to the total number of thermostats. This way a proper sampling of phase space is ensured, even if the various vibrational modes of the molecule(s) are only weakly coupled to the heat bath.

The thermostat for the electrons should be adjusted so that the target ‘temperature’ should be roughly the average value of EKINC in the later part of previous uncontrolled simulation. Good values for the characteristic frequency of the electrons and ions here are 10000.0 to 15000.0 and 2500.0 to 4000.0, respectively.

If you want to restart with active Nose thermostats, you need to read the state of the thermostat from the restart as well with adding NOSEE and NOSEP to the RESTART keyword for the electron and ion thermostats. If you change the thermostat algorithm (i.e. turn it on or off) you should not use those keywords and use RESCALE OLD VELOCITIES instead.

Based on the information presented in the section (and additional help from the CPMD manual if needed) we want to continue the previously uncontrolled CP-MD simulation of the glycine molecule with Nose thermostats for the electrons and atoms (at 300K). If the microcanonical CP-MD run from the previous run is not yet finished, you can initiate a graceful exit (i.e. one the produces a restart file) by creating a file named EXIT in the working directory of the CPMD run: e.g. by typing

touch EXIT


: > EXIT


echo > EXIT

Input files: 4-gly-md-nvt.inp and 5-gly-md-rotcor.inp.