[gmx-users] kinetically trapped in a local minimum???
#NGUYEN CONG TRI#
NGUY0045 at ntu.edu.sg
Sat Mar 15 16:29:06 CET 2008
Thank you very much for your valuable advice.
From: gmx-users-bounces at gromacs.org on behalf of Mark Abraham
Sent: Sat 3/15/2008 8:51 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] kinetically trapped in a local minimum???
#NGUYEN CONG TRI# wrote:
> Dear Gromacs users,
> How can we know that the system is properly equilibrated or whether we
> should extend the equilibration step. Someone suggest that we look at
> the potential energy to see whether it has converged? Is it correct?
That's one test. You should look for converged behaviour in a range of
simulation observables that hopefully include those that will indicate
that the observable(s) on which you plan to collect data in the
production run are/will be showing equilibrated behaviour.
> One more question, normally, we carry out the equilibration at 300K,
> don't we?
If you're interested in a room-temperature system, that would be a
logical choice. If you're interested in another temperature, be aware
that most force fields are not parametrized on data from other temperatures.
> How can we know that this temperature is enough and the system
> is not kinetically trapped in a local minimum? And if it is whether it
> affects the production run later on?
You can't ever tell from a single simulation in isolation. You can try a
cheaper simulation at a higher-temperature or coarser-graining to get an
idea how big the system space might be, or do simulated annealing (or
other such nonlocal-search approaches), but there's never a guarantee
that these reflect what's accessible in a dynamical system. An
implicit-solvent replica-exchange MD simulation (e.g. with AMBER) can be
instructive. Experience with similar systems can be a guide also.
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