On easy implementation of a variant of the replica exchange with solute tempering in GROMACS

Abstract

To reduce the number of replicas required in the conventional replica exchange method for huge systems, recently the replica exchange with solute tempering (REST) method was proposed. Here we showed that a variant of REST realized by rescaling the force-field parameters can be performed with GROMACS 4 without changing the code. We tested the variant REST for alanine dipeptide and an N-terminal peptide from p53 confirming its performance nearly equal to the original REST.

Molecular mechanisms for intrafibrillar collagen mineralization in skeletal tissues

“…HREMD simulation [26,27] was used to investigate cluster formation to explore whether the packed collagen molecules in the fibril can act as a nucleating template for HAP formation. A total of 28 replicas was used and an exchange attempt was made every 1 ps, for all even and odd replica pairs in an alternating fashion (20 ns for each replica), with exchange acceptance ratios between 17% and 25% (SI 1.3).…”

Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms

“…To overcome this problem, the replica exchange with solute tempering (REST) method has been proposed, in which only the solute molecule is heated up, while the solvent stays cold even in high temperature replicas [70]. REST is one of Hamiltonian REMD methods, where solute tempering is achieved by scaling solute–solvent and solvent–solvent interactions (REST1) [70] or solute–solvent and solute–solute interactions (REST2) [190,191]. …”

“…To overcome this problem, REST2 has been developed [190,191], in which the potential energy of the system for replica m is given by $$E_{m}false(qfalse)=\frac{{\beta }_m}{{\beta }_0}{E}_{\mathit{pp}}false(qfalse)+\sqrt{\frac{{\beta }_m}{{\beta }_0}}{E}_{\mathit{pw}}false(qfalse)+E_{\mathit{ww}}false(qfalse),$$and the acceptance criterion for the replica exchange becomes $$\begin{array}{ccc}left\Delta & =& false({\beta }_m-{\beta }_{n}false)\\ & & \times \left[(E_{\mathit{pp}}false(q_{n}false)-E_{\mathit{pp}}false(q_{m}false))+\frac{\sqrt{{\beta }_0}}{\sqrt{{\beta }_m}+\sqrt{{\beta }_n}}false(E_{\mathit{pw}}false(q_{n}false)-E_{\mathit{pw}}false(q_{m}false)false)\right].\end{array}$$…”

Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration

“…Several recipes for choosing the modified Hamiltonian have been proposed in the literature [207][208][209][210][211][212][213][214][215][216][217][218][219]. Among these, a notable idea is that of solute tempering [208,217] which is used for the simulation of solvated biomolecules.…”