Adaptive single replica multiple state transition interface sampling.

نویسندگان

  • Wei-Na Du
  • Peter G Bolhuis
چکیده

The multiple state transition path sampling method allows sampling of rare transitions between many metastable states, but has the drawback that switching between qualitatively different pathways is difficult. Combination with replica exchange transition interface sampling can in principle alleviate this problem, but requires a large number of simultaneous replicas. Here we remove these drawbacks by introducing a single replica sampling algorithm that samples only one interface at a time, while efficiently walking through the entire path space using a Wang-Landau approach or, alternatively, a fixed bias. We illustrate the method on several model systems: a particle diffusing in a simple 2D potential, isomerization in a small Lennard Jones cluster, and isomerization of the alanine dipeptide in explicit water.

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

UvA - DARE ( Digital Academic Repository ) Adaptive single replica multiple state transition interface sampling

Disclaimer/Complaints regulations If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: http://uba.uva.nl/en/contact, or a letter to: Library of ...

متن کامل

A replica exchange transition interface sampling method with multiple interface sets for investigating networks of rare events.

The multiple state transition interface sampling (TIS) framework in principle allows the simulation of a large network of complex rare event transitions, but in practice suffers from convergence problems. To improve convergence, we combine multiple state TIS [J. Rogal and P. G. Bolhuis, J. Chem. Phys. 129, 224107 (2008)] with replica exchange TIS [T. S. van Erp, Phys. Rev. Lett. 98, 268301 (200...

متن کامل

Multiple-Replica Strategies for Free-Energy Calculations in NAMD: Multiple-Walker Adaptive Biasing Force and Walker Selection Rules.

From the most powerful supercomputers to multicore desktops and laptops, parallel computing architectures have been in the mainstream for some time. However, numerical schemes for calculating free energies in molecular systems that directly leverage this hardware paradigm, usually taking the form of multiple-replica strategies, are just now on the cusp of becoming standard practice. Here, we pr...

متن کامل

Equilibrium kinetic network of the villin headpiece in implicit solvent.

We applied the single-replica multiple-state transition-interface sampling method to elucidate the equilibrium kinetic network of the 35-residue-fragment (HP-35) villin headpiece in implicit water at room temperature. Starting from the native Protein Data Bank structure, nine (meta)stable states of the system were identified, from which the kinetic network was built by sampling pathways between...

متن کامل

Sampling the equilibrium kinetic network of Trp-cage in explicit solvent.

We employed the single replica multiple state transition interface sampling (MSTIS) approach to sample the kinetic (un)folding network of Trp-cage mini-protein in explicit water. Cluster analysis yielded 14 important metastable states in the network. The MSTIS simulation thus resulted in a full 14 × 14 rate matrix. Analysis of the kinetic rate matrix indicates the presence of a near native inte...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

عنوان ژورنال:
  • The Journal of chemical physics

دوره 139 4  شماره 

صفحات  -

تاریخ انتشار 2013