[gmx-users] Re: some questions about side chain dihedral angle sampling

mircial at sjtu.edu.cn mircial at sjtu.edu.cn
Fri Mar 9 10:01:19 CET 2012

I forget to say that, there are other residues around that residue whose side chain coformations will affect each others, So, it is difficult to use umbrella sampling method....


----- 原始邮件 -----
发件人: mircial at sjtu.edu.cn
收件人: gmx-users at gromacs.org
发送时间: 星期五, 2012年 3 月 09日 下午 4:58:02
主题: some questions about side chain dihedral angle sampling

Dear All:

I am doing molecular dynamics simulations of a protein. In my system, there is a critical residue which is important for its activity. I want to sample the side chain conformations of this residue, i.e., calculate the most favourable side chain dihedral angles of this residue and calculate the energy barriers when its side chain conformation changes. Since common MD simulations is too slow to sample all of the possible conformations, my question is does there any methods that can do this kind of sampling quickly in GROMACS? Does Locally Enhanced Molecular Dynamics a proper method? Does there any other possible method?

Thanks in advance for all of your helps!

Best Regards

Ruo-Xu Gu

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