使用GROMACS实现二聚体代谢物
Implementing Dimer Metadynamics using GROMACS
摘要：
我们开发了二聚体代谢物的Gromacs实现[JCTC 13，425（2017）]，通过人工离域效应增强采样。该实现完全基于为此目的开发的Plumed集体变量，Gromacs输入参数的微调，修改的力场和自定义非键合相互作用。我们证明了这种实现在真空中和水中的丙氨酸二肽，并在水中的12个残基的丙氨酸多肽和比较的结果与一个标准的多副本技术，如平行回火。在所有考虑的情况下，这种比较是一致的，并且二聚体元动力学的结果更平滑，需要更短的模拟，从而证明了Gromacs实现的一致性和有效性。
英文摘要：
We develop a Gromacs implementation of Dimer Metadynamics[JCTC 13, 425 (2017)] for enhanced sampling through artificial delocalization effects. This implementation is based entirely on a Plumed collective variable developed for this purpose, the fine tuning of Gromacs input parameters, modified forcefields and custom non-bonded interactions. We demonstrate this implementation on Alanine Dipeptide in vacuum and in water, and on the 12-residue Alanine Polypeptide in water and compare the results with a standard multiple-replica technique such as Parallel Tempering. In all the considered cases this comparison is consistent and the results with Dimer Metadynamics are smoother and require shorter simulations, thus proving the consistency and effectiveness of this Gromacs implementation.
机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。
