# [gmx-users] Calculate RMSD for specific residue.

Tue Aug 19 14:24:26 CEST 2014

```Great, it's working. I wasn't sure whether I still can do it after
simulation run.

2014-08-19 13:21 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 8/19/14, 8:17 AM, Dawid das wrote:
>
>> 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?
>>
>>
> That's exactly how index groups work.
>
> -Justin
>
>
>
>> 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
>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 601
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
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```