Constrained molecular dynamics: Difference between revisions

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== References ==
== References ==
<references>
<references>
<ref name="Ryckaert77">[http://dx.doi.org/10.1016/0021-9991(77)90098-5 J. P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, J. Comp. Phys. 23, 327 (1977).]</ref>
<ref name="Carter89">[http://dx.doi.org/10.1016/S0009-2614(89)87314-2 E. A. Carter, G. Ciccotti, J. T. Hynes, and R. Kapral, Chem. Phys. Lett. 156, 472 (1989).]</ref>
<ref name="Otter00">[http://dx.doi.org/10.1080/00268970009483348 W. K. Den Otter and W. J. Briels, Mol. Phys. 98, 773 (2000).]</ref>
<ref name="Darve02">[http://dx.doi.org/10.1080/08927020211975 E. Darve, M. A. Wilson, and A. Pohorille, Mol. Simul. 28, 113 (2002).]</ref>
<ref name="Fleurat05">[http://dx.doi.org/10.1063/1.1948367 P. Fleurat-Lessard and T. Ziegler, J. Chem. Phys. 123, 084101 (2005).]</ref>
<ref name="Ryckaert77">[http://dx.doi.org/10.1016/0021-9991(77)90098-5 J. P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, J. Comp. Phys. 23, 327 (1977).]</ref>
<ref name="Ryckaert77">[http://dx.doi.org/10.1016/0021-9991(77)90098-5 J. P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, J. Comp. Phys. 23, 327 (1977).]</ref>
</references>
</references>

Revision as of 14:23, 18 April 2022

Constrained molecular dynamics is performed using the SHAKE algorithm.[1]. In this algorithm, the Lagrangian for the system [math]\displaystyle{ \mathcal{L} }[/math] is extended as follows:

[math]\displaystyle{ \mathcal{L}^*(\mathbf{q,\dot{q}}) = \mathcal{L}(\mathbf{q,\dot{q}}) + \sum_{i=1}^{r} \lambda_i \sigma_i(q), }[/math]

where the summation is over r geometric constraints, [math]\displaystyle{ \mathcal{L}^* }[/math] is the Lagrangian for the extended system, and λi is a Lagrange multiplier associated with a geometric constraint σi:

[math]\displaystyle{ \sigma_i(q) = \xi_i({q})-\xi_i \; }[/math]

with ξi(q) being a geometric parameter and ξi is the value of ξi(q) fixed during the simulation.

In the SHAKE algorithm, the Lagrange multipliers λi are determined in the iterative procedure:

  1. Perform a standard MD step (leap-frog algorithm):
    [math]\displaystyle{ v^{t+{\Delta}t/2}_i = v^{t-{\Delta}t/2}_i + \frac{a^{t}_i}{m_i} {\Delta}t }[/math]
    [math]\displaystyle{ q^{t+{\Delta}t}_i = q^{t}_i + v^{t+{\Delta}t/2}_i{\Delta}t }[/math]
  2. Use the new positions q(t+Δt) to compute Lagrange multipliers for all constraints:
    [math]\displaystyle{ {\lambda}_k= \frac{1}{{\Delta}t^2} \frac{\sigma_k(q^{t+{\Delta}t})}{\sum_{i=1}^N m_i^{-1} \bigtriangledown_i{\sigma}_k(q^{t}) \bigtriangledown_i{\sigma}_k(q^{t+{\Delta}t})} }[/math]
  3. Update the velocities and positions by adding a contribution due to restoring forces (proportional to λk):
    [math]\displaystyle{ v^{t+{\Delta}t/2}_i = v^{t-{\Delta}t/2}_i + \left( a^{t}_i-\sum_k \frac{{\lambda}_k}{m_i} \bigtriangledown_i{\sigma}_k(q^{t}) \right ) {\Delta}t }[/math]
    [math]\displaystyle{ q^{t+{\Delta}t}_i = q^{t}_i + v^{t+{\Delta}t/2}_i{\Delta}t }[/math]
  4. repeat steps 2-4 until either |σi(q)| are smaller than a predefined tolerance (determined by SHAKETOL), or the number of iterations exceeds SHAKEMAXITER.

Anderson thermostat

  • For a constrained molecular dynamics run with Andersen thermostat, one has to:
  1. Set the standard MD-related tags: IBRION=0, TEBEG, POTIM, and NSW.
  2. Set MDALGO=1, and choose an appropriate setting for ANDERSEN_PROB.
  3. Define geometric constraints in the ICONST-file, and set the STATUS parameter for the constrained coordinates to 0.
  4. When the free-energy gradient is to be computed, set LBLUEOUT=.TRUE.

References

  1. ↑ J. P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, J. Comp. Phys. 23, 327 (1977).
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