Dear all, I have some doubt regarding energy minimization and the use of constraint algorithms (such as LINCS) that may come from my inexperience in GROMACS and molecular dynamics in general.
In a Berk Hess talk given at the GROMACS workshop 2007 it is stated: (https://extras.csc.fi/chem/courses/gmx2007/Berk_talks/forcef.pdf) "In GROMACS bonds are usually replaced by constraints, i.e. the distances between bonded atoms are fixed to their equilibrium value. Constraints are actually a more faithful representation of reality since the dynamics of bonds is of quantum nature..” In an article about the use of SHAKE (another algorithm for constraints) I read that: "Iinitiating a constrained simulation from an unconstrained minimum usually results in spurious temperature fluctuations that slow down the equilibration of the molecule and/or introduce artifacts" (Duan, Y., Kumar, S., Rosenberg, J.M. and Kollman, P.A. "Gradient SHAKE: An improved method for constrained energy minimization in macromolecular simulations." Journal of Computational Chemistry (2004), 16(11): 1351-1356.) That suggests to me that the use of constraints during EM is somehow suggested. However why use constraints (that maintain fixed lengths of the selected bonds) during this step of the simulation if what you want to achieve with EM is the local potential energy minimum and it is required to have a high degree of freedom in the atoms' movement? Is my interpretation of the use of constraints wrong? Sorry for the long email, any suggestion from an expert point of view is welcome. Thanks -- Irene Farabella Wellcome Trust PhD student Institute of Structural and Molecular Biology Department of of Biological Sciences Birkbeck University of London Malet Street London WC1E 7HX Telephone +44 (0)20 7631 6815 -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
