[gmx-users] RMSD calculation in protein

David van der Spoel spoel at xray.bmc.uu.se
Thu Apr 22 09:41:02 CEST 2004

On Thu, 2004-04-22 at 05:30, zhang xudong wrote:
> Dearl all
>  I finish a protein MD simulation  and want to analysis data using gromacs 
> analysis tools.  my reasch work aim to a part or a domain of the 
> protein,not whole protein. It is first time using these analysis tools. 
> so,there are two questions as follows i want to consult about RMSD 
> calculation:
> 1.How can i draw a RMSD plot which represents a part of the protein(such as 
> several amino acid residues)?
make an index filewith the subset of your protein
(make_ndx -f conf.gro)

> 2.are there other analysis tool i can use to draw such a RMSD plot rather 
> than  gromacs analysis tool?
maybe, but probably more complicated.
> thanks in advance
> XuDong Zhang
> Department of Biology
> The University of YunNan,china
> zxdcs01 at hotmail.com
> zhangxd at ynu.edu.cn
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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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