dt t Specifies the timestep (fs) (defaults to 1 fs) time t Specifies the simulation duration (ns) (defaults to 1ns) numerical-tetra is similar to -numerical, but numerical differentiation uses points in a tetrahedron instead of points in an octahedron numerical Configures the simulation to use numerical differentiation of the potential energy (defaults to analytical solving) Specifies the path to the substrate to simulate The installation process requires the C standard library, a C99-compliant compiler, and GNU Make. Should you want to go ahead with the default settings, compilation is achieved on UNIX systems using the provided Makefile. This is done by editing the constants in headers/config.h. You might first want to configure SENPAI for your machine and use case. Inspired by the AMBER family of force fields, it allows SENPAI to compute forces with unprecedented efficiency. No extra libraries are required!Įfficient computing model: the ONICHaN (Optimized Numerical Integration, Classical Harmonics, and N-body) model was tailored for SENPAI over months of work. Simulations are rendered as XYZ, and can be immediately viewed using existing software without prior conversion!įull C99 compliance, no libraries needed: SENPAI is 100% compliant with the C99 standard. Quickly and easily prepare simulations and adjust them with no hassle. No complicated file formats: The MDS, MDM, and MDP file formats developped for SENPAI can be hand-written! No need for special software. Should you prefer numerical potential differentiation, SENPAI offers two different numerical differentiation methods which can be configured as well! SENPAI analytically solves for the force vector, resulting in an extreme speedup. No potential differentiation: Traditional MD simulators compute a particle's total potential and numerically differentiate it to compute the applied force. SENPAI sequentially runs several algorithms like gradient descent to properly set the system up for simulation. Integrated potential reduction: Easily mitigate the issue of "garbage in, garbage out"! If told to do so, SENPAI will reduce the potential energy of the system to a user-selected target value before simulating. SENPAI being used with VMD to simulate a urea-ChCl deep eutectic solvent Keeping it simple SENPAI is licensed under the terms of the GPLv3.
It provides a way to simulate molecular systems of educative and academic interest on devices ranging from personal laptops to purpose-built mainframes. SENPAI is a flexible, highly-configurable molecular dynamics (MD) simulation software aimed at students and academia. SENPAI - Simplified Evolutive N-body Processing and Analytics for Integration