[gmx-users] Calculate RMSD for specific residue.

[Dawid das]

Right, I figured that out but in my groups when I run g_rms:

Group     0 (         System) has 32645 elements
Group     1 (        Protein) has  3470 elements
Group     2 (      Protein-H) has  1772 elements
Group     3 (        C-alpha) has   217 elements
Group     4 (       Backbone) has   653 elements
Group     5 (      MainChain) has   869 elements
Group     6 (   MainChain+Cb) has  1065 elements
Group     7 (    MainChain+H) has  1076 elements
Group     8 (      SideChain) has  2394 elements
Group     9 (    SideChain-H) has   903 elements
Group    10 (    Prot-Masses) has  3461 elements
Group    11 (    non-Protein) has 29175 elements
Group    12 (          Water) has 29115 elements
Group    13 (            SOL) has 29115 elements
Group    14 (      non-Water) has  3530 elements
Group    15 (            Ion) has    60 elements
Group    16 (             NA) has    31 elements
Group    17 (             CL) has    29 elements
Group    18 ( Water_and_ions) has 29175 elements

I don't have a group I am interested in. Should I create new index.ndx
file? If so can I create it after the simulation, add new atoms group (CH6
residue)  and extract the information from simulation for my CH6 residue?


2014-08-19 13:12 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 8/19/14, 8:10 AM, Dawid das wrote:
>
>> Dear Gromacs experts,
>>
>> How can I calculate RMSD as a fucntion of time for one residue in my
>> protein? Let's say I have a part of my sequence:
>> ...-Phe-Ala-Ser-CH6-Tyr-Met-Cys-Gly-... . Now I want to get a plot of
>> RMSD
>> versus time for CH6 (my newly introduced residue).
>> I can't find such an option in g_rms and what g_rmsf -od is not what I am
>> interested in or I understood something incorrectly.
>>
>>
> g_rms will do whatever you want if you provide the right index group.
>
> -Justin
>
> --
> ==================================================
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
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