[gmx-users] Constraints and EM

Berk Hess gmx3 at hotmail.com
Fri Feb 26 14:52:49 CET 2010


This all depends on what you want to achieve.
In most cases energy minimization is used to remove atomic overlap from
a bad starting structure or from slightly overlapping solvent atoms.
If you run your MD with constraints, you probably also want constraints
during the (last) minimization step. Otherwise the effects mentioned
in the reference you gave might be important.

Only rarely people are interested in really arriving at the (local) energy minimum.
Note that this is only relevant at 0K, which is not the most interesting condition.
A notable exception in normal mode analysis, where the method requires
a conformation very close to a local minimum.


> Date: Fri, 26 Feb 2010 09:53:02 +0000
> From: i.farabella at mail.cryst.bbk.ac.uk
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Constraints and EM
> 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
> -- 
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