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....
Regards ----- 原始邮件 ----- 发件人: [email protected] 收件人: [email protected] 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 -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
