764 research outputs found
Free energy calculations of a proton transfer reaction by simulated tempering umbrella sampling first principles molecular dynamics simulations
A new simulated tempering method, which is referred to as simulated tempering
umbrella sampling, for calculating the free energy of chemical reactions is
proposed. First principles molecular dynamics simulations with this simulated
tempering were performed in order to study the intramolecular proton transfer
reaction of malonaldehyde in aqueous solution. Conformational sampling in
reaction coordinate space can be easily enhanced with this method, and the free
energy along a reaction coordinate can be calculated accurately. Moreover, the
simulated tempering umbrella sampling provides trajectory data more efficiently
than the conventional umbrella sampling method.Comment: 5 pages, (Revtex4-1), 3 figure
Amino-acid-dependent main-chain torsion-energy terms for protein systems
Many commonly used force fields for protein systems such as AMBER, CHARMM,
GROMACS, OPLS, and ECEPP have amino-acid-independent force-field parameters of
main-chain torsion-energy terms. Here, we propose a new type of
amino-acid-dependent torsion-energy terms in the force fields. As an example,
we applied this approach to AMBER ff03 force field and determined new
amino-acid-dependent parameters for and angles for each amino
acid by using our optimization method, which is one of the knowledge-based
approach. In order to test the validity of the new force-field parameters, we
then performed folding simulations of -helical and -hairpin
peptides, using the optimized force field. The results showed that the new
force-field parameters gave structures more consistent with the experimental
implications than the original AMBER ff03 force field.Comment: 10 pages, (Revtex4.1), 3 tables, 6 figure
Generalized-Ensemble Algorithms for the Isobaric-Isothermal Ensemble
We present generalized-ensemble algorithms for isobaric-isothermal molecular
simulations. In addition to the multibaric-multithermal algorithm and
replica-exchange method for the isobaric-isothermal ensemble, which have
already been proposed, we propose a simulated tempering method for this
ensemble. We performed molecular dynamics simulations with these algorithms for
an alanine dipeptide system in explicit water molecules to test the
effectiveness of the algorithms. We found that these generalized-ensemble
algorithms are all useful for conformational sampling of biomolecular systems
in the isobaric-isothermal ensemble.Comment: 6 pages, (Revtex4), 4 figure
Replica-Exchange Molecular Dynamics Simulations for Various Constant Temperature Algorithms
In the replica-exchange molecular dynamics method, where constant-temperature
molecular dynamics simulations are performed in each replica, one usually
rescales the momentum of each particle after replica exchange. This rescaling
method had previously been worked out only for the Gaussian constraint method.
In this letter, we present momentum rescaling formulae for four other commonly
used constant-temperature algorithms, namely, Langevin dynamics, Andersen
algorithm, Nos\'{e}-Hoover thermostat, and Nos\'{e}-Poincar\'{e} thermostat.
The effectiveness of these rescaling methods is tested with a small
biomolecular system, and it is shown that proper momentum rescaling is
necessary to obtain correct results in the canonical ensemble.Comment: 6 pages, (Revtex4), 4 figure
Multicanonical Algorithm, Simulated Tempering, Replica-Exchange Method, and All That
We discuss multi-dimensional generalizations of multicanonical algorithm,
simulated tempering, and replica-exchange method. We generalize the original
potential energy function by adding any physical quantity of interest
as a new energy term with a coupling constant . We then perform a
multi-dimensional multicanonical simulation where a random walk in and
space is realized. We can alternately perform a multi-dimensional simulated
tempering simulation where a random walk in temperature and parameter
is realized. The results of the multi-dimensional replica-exchange
simulations can be used to determine the weight factors for these
multi-dimensional multicanonical and simulated tempering simulations.Comment: 4 pages, (Revtex4), 2 figure
Designed-walk replica-exchange method for simulations of complex systems
We propose a new implementation of the replica-exchange method (REM) in which
replicas follow a pre-planned route in temperature space instead of a random
walk. Our method satisfies the detailed balance condition in the proposed
route. The method forces tunneling events between the highest and lowest
temperatures to happen with an almost constant period. The number of tunneling
counts is proportional to that of the random-walk REM multiplied by the square
root of moving distance in temperature space. We applied this new
implementation to two kinds of REM and compared the results with those of the
conventional random-walk REM. The test system was a two-dimensional Ising
model, and our new method reproduced the results of the conventional
random-walk REM and improved the tunneling counts by three times or more than
that of the random-walk REM.Comment: 6 pages, 3 figures, 1 table; methods are the same before, but results
and some references are added, table is update
An Efficient Simulation Protocol for Determining the Density of States: Combination of Replica-Exchange Wang-Landau Method and Multicanonical Replica-Exchange Method
By combining two generalized-ensemble algorithms, Replica-Exchange
Wang-Landau (REWL) method and Multicanonical Replica-Exchange Method (MUCAREM),
we propose an effective simulation protocol to determine the density of states
with high accuracy. The new protocol is referred to as REWL-MUCAREM, and REWL
is first performed and then MUCAREM is performed next. In order to verify the
effectiveness of our protocol, we performed simulations of a square-lattice
Ising model by the three methods, namely, REWL, MUCAREM, and REWL-MUCAREM. The
results showed that the density of states obtained by the REWL-MUCAREM is more
accurate than that is estimated by the two methods separately.Comment: 12 pages, , (Revtex4-1), 5 figure
Optimizations of protein force fields
In this Chapter we review our works on force fields for molecular simulations
of protein systems. We first discuss the functional forms of the force fields
and present some extensions of the conventional ones. We then present various
methods for force-field parameter optimizations. Finally, some examples of our
applications of these parameter optimization methods are given and they are
compared with the results from the existing force-fields.Comment: 56 pages, (Springer Verlag global LaTeX2e support for multi authored
books), 28 figures, 13 table
Deterministic replica-exchange method without pseudo random numbers for simulations of complex systems
We propose a replica-exchange method (REM) which does not use pseudo random
numbers. For this purpose, we first give a conditional probability for Gibbs
sampling replica-exchange method (GSREM) based on the heat bath method. In
GSREM, replica exchange is performed by conditional probability based on the
weight of states using pseudo random numbers. From the conditional probability,
we propose a new method called deterministic replica-exchange method (DETREM)
that produces thermal equilibrium distribution based on a differential equation
instead of using pseudo random numbers. This method satisfies the detailed
balance condition using a conditional probability of Gibbs heat bath method and
thus results can reproduce the Boltzmann distribution within the condition of
the probability. We confirmed that the equivalent results were obtained by REM
and DETREM with two-dimensional Ising model. DETREM can avoid problems of
choice of seeds in pseudo random numbers for REM using a differential equation.Comment: 12 pages, 1 table, 11 figures, auto-correlation function and time
series of internal state are adde
Application of Simulated Tempering and Magnetizing to a Two-Dimensional Potts Model
We applied the simulated tempering and magnetizing (STM) method to the
two-dimensional three-state Potts model in an external magnetic field in order
to perform further investigations of the STM's applicability. The temperature
as well as the external field are treated as dynamical variables updated during
the STM simulations. After we obtained adequate information for several lattice
sizes (up to ), we also performed a number of conventional
canonical simulations of large lattices, especially in order to illustrate the
crossover behavior of the Potts model in external field with increasing .
The temperature and external field for larger lattice size simulations were
chosen by extrapolation of the detail information obtained by STM. We carefully
analyzed the crossover scaling at the phase transitions with respect to the
lattice size as well as the temperature and external field. The crossover
behavior is clearly observed in the simulations in agreement with theoretical
predictions.Comment: 21 pages, 21 figure
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