[gmx-users] questions about normal mode analysis in gromacs

凌未风 grx1985 at qq.com
Wed Dec 3 23:31:50 CET 2014

Hi All:

I have pasted my questions before, but unfortunately no one  reply me, so I am trying to make my questions clear and concise here. Hope some one can help me. :)

I am using normal mode analysis to analyze conformational changes of proteins. I am trying to use g_nmtraj to generate virtual trajectories along each normal modes. I have the following questions now:

1, Does anyone know where I can find the algorithm of g_nmtraj command? I am asking this because I found some differences between the trajectories generated by g_nmtraj and other tools, so I am curious about the algorithm used by g_nmtraj. 

2, There is a parameter named of "-phases". Does anyone know what does this parameter mean?

Really look forward to hearing from you. Thanks a lot. 


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