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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 is extended as follows:
where the summation is over r geometric constraints, is the Lagrangian for the extended system, and λi is a Lagrange multiplier associated with a geometric constraint σi:
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:
- Perform a standard MD step (leap-frog algorithm):
- Use the new positions q(t+Δt) to compute Lagrange multipliers for all constraints:
- Update the velocities and positions by adding a contribution due to restoring forces (proportional to λk):
- 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:
- Set the standard MD-related tags: IBRION=0, TEBEG, POTIM, and NSW.
- Set MDALGO=1, and choose an appropriate setting for ANDERSEN_PROB.
- Define geometric constraints in the ICONST-file, and set the STATUS parameter for the constrained coordinates to 0.
- When the free-energy gradient is to be computed, set LBLUEOUT=.TRUE.
References