Conformational search using Gromacs

zako

Hello Everyone in the forum,when i was doing little search about "conformational search", I found a method describing how to use Gromacs to perform conformational search, I wonder if is it a good method or not ?

Method link : http://www.ag.kagawa-u.ac.jp/charlesy/memo/conformational-search/

sobereva

GROMACS can at most be used for conformation sampling, it is absolutely inacceptable for conformation search purpose, because accuracy of almost all existing forcefields is too poor. For example, see Int J Quantum Chem. 2018;118:e25512 (https://doi.org/10.1002/qua.25512) for comprehensive benchmarking. Even semi-empirical methods such as PM7 and GFN-xTB are not able to reliably distinguish lowest conformers in most cases.

Molclus is a very ideal code for performing conformation search, see http://www.keinsci.com/research/molclus.html, it has already been utilized in many publications.
Relevant tutorials:
使用molclus程序做团簇构型搜索和分子构象搜索
http://bbs.keinsci.com/thread-577-1-1.html
gentor：扫描方式做分子构象搜索的便捷工具
http://bbs.keinsci.com/thread-2388-1-1.html
将Confab或Frog2与Molclus联用对有机体系做构象搜索
http://bbs.keinsci.com/thread-20063-1-1.html
使用Molclus结合xtb做的动力学模拟对瑞德西韦(Remdesivir)做构象搜索
http://bbs.keinsci.com/thread-16255-1-1.html

Currently English version of molclus manual and tutorial is not available, but will be released in this year.