[gmx-users] how to calculate redisue wise RMSD in gromacs?

TJ Piggot t.piggot at bristol.ac.uk
Fri Mar 28 13:48:32 CET 2008

Also try g_rmsf -h. This might be what you are looking for.


--On Friday, March 28, 2008 15:07:02 +1100 Mark Abraham 
<Mark.Abraham at anu.edu.au> wrote:

> yren at home.ipe.ac.cn wrote:
>> Dear friends,
>>  I have carried out a simulation of a protein in solution and want to
>> analyse redisue wise root-mean-square-deviation (RMSD) of the protein. As
>> far as I know,   RMSD can be calculated by g_rms, which gives RMSD as a
>> function of time, but what I expect is RMSD as a function of residue
>> number. It's said that AMBER has this function. I wonder whether gromacs
>> can do this also.
> Check out "g_rms -h", in particular the -ng option. I expect you can use
> this in concert with an index file that has a group for each residue.
> Mark
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TJ Piggot
t.piggot at bristol.ac.uk
University of Bristol, UK.

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