اشترك بالحزمة الذهبية واحصل على وصول غير محدود شمرا أكاديميا
تسجيل مستخدم جديدReplica-Permutation Method with the Suwa-Todo Algorithm beyond the Replica-Exchange Method
116
0
0.0
(
0
)
اسأل ChatGPT حول البحث
ﻻ يوجد ملخص باللغة العربية
We propose a new method for molecular dynamics and Monte Carlo simulations, which is referred to as the replica-permutation method (RPM), to realize more efficient sampling than the replica-exchange method (REM).In RPM not only exchanges between two replicas but also permutations among more than two replicas are performed. Furthermore, instead of the Metropolis algorithm, the Suwa-Todo algorithm is employed for replica-permutation trials to minimize its rejection ratio. We applied RPM to particles in a double-well potential energy, Met-enkephalin in vacuum, and a C-peptide analog of ribonuclease A in explicit water. For a comparison purposes, replica-exchange molecular dynamics simulations were also performed. As a result, RPM sampled not only the temperature space but also the conformational space more efficiently than REM for all systems. From our simulations of C-peptide, we obtained the alpha-helix structure with salt-bridges between Gly2 and Arg10 which is known in experiments. Calculating its free-energy landscape, the folding pathway was revealed from an extended structure to the alpha-helix structure with the salt-bridges. We found that the folding pathway consists of the two steps: The first step is the salt-bridge formation step, and the second step is the alpha-helix formation step.
قيم البحث
اقرأ أيضاً
We propose two efficient algorithms for configurational sampling of systems with rough energy landscape. The first one is a new method for the determination of the multicanonical weight factor. In this method a short replica-exchange simulation is
performed and the multicanonical weight factor is obtained by the multiple-histogram reweighting techniques. The second one is a further extension of the first in which a replica-exchange multicanonical simulation is performed with a small number of replicas. These new algorithms are particularly useful for studying the protein folding problem.
In finite-size scaling analyses of Monte Carlo simulations of second-order phase transitions one often needs an extended temperature/energy range around the critical point. By combining the replica-exchange algorithm with cluster updates and an adapt
ive routine to find the range of interest, we introduce a new flexible and powerful method for systematic investigations of critical phenomena. As a result, we gain two further orders of magnitude in the performance for 2D and 3D Ising models in comparison with the recently proposed Wang-Landau recursion for cluster algorithms based on the multibondic algorithm, which is already a great improvement over the standard multicanonical variant.
We estimated the residual entropy of ice Ih by the recently developed simulation protocol, namely, the combination of Replica-Exchange Wang-Landau algorithm and Multicanonical Replica-Exchange Method. We employed a model with the nearest neighbor int
eractions on the three-dimensional hexagonal lattice, which satisfied the ice rules in the ground state. The results showed that our estimate of the residual entropy is found to be within 0.038 % of series expansion estimate by Nagle and within 0.000077 % of PEPS algorithm by Vanderstraeten. In this article, we not only give our latest estimate of the residual entropy of ice Ih but also discuss the importance of the uniformity of a random number generator in MC simulations.
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.
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 for
ces 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.
سجل دخول لتتمكن من نشر تعليقات
التعليقات
جاري جلب التعليقات
سجل دخول لتتمكن من متابعة معايير البحث التي قمت باختيارها
