[gmx-users] Can I specify the residue numbers for RMSD?

[Justin Lemkul]

On 8/14/17 8:15 AM, ZHANG Cheng wrote:
> Dear Gromacs,
> My MD contains a protein (442 residues) and 203 free glycines. The numbering of the residues is:
>
>
> 1-442: the protein residues
> 443-645: the 203 free glycines
>
>
> When I use the "rms" command, all the 645 residues are considered as the "Protein" category.
>
>
> I cannot find an option that could only calculate rmsd for the first 442 residues in my proteins. How can I do this? Thank you.

Create an index group with gmx make_ndx or gmx select.

-Justin

>
> Group     0 (         System)
> Group     1 (        Protein)
> Group     2 (      Protein-H)
> Group     3 (        C-alpha)
> Group     4 (       Backbone)
> Group     5 (      MainChain)
> Group     6 (   MainChain+Cb)
> Group     7 (    MainChain+H)
> Group     8 (      SideChain)
> Group     9 (    SideChain-H)
> Group    10 (    Prot-Masses)
> Group    11 (    non-Protein)
> Group    12 (          Water)
> Group    13 (            SOL)
> Group    14 (      non-Water)
> Group    15 (            Ion)
> Group    16 (             NA)
> Group    17 (             CL)
> Group    18 ( Water_and_ions)

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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