I want to do Umbrella Sampling (US) using NAMD, my confusion is as follows:
1. US can be perform using SMD, therefore, how to decide the SMD config file input is correct or not? What input CV or CF is required? If I want to perform for specific number of molecule the COM is dependent on it ?
2. The SMD, MMPBSA, ABF are all giving same results, which is best among all of them?
I want to do Steered Molecular Dynamics with umbrella sampling. Can anyone help me with examples or scripts ?
Abhishek Tyagi
@Hong Zhu What cases you are indicating about the ABF and US. I read that US give more better sampling of multiple MDs
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Jamoliddin Razzokov
Take a look the following link:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html
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