[gmx-users] Calculate RMSD for specific residue.

[Justin Lemkul]

On 8/19/14, 8:24 AM, Dawid das wrote:
> Great, it's working. I wasn't sure whether I still can do it after
> simulation run.
>

Use of index files is not limited to the simulation itself; this is covered 
quite extensively in the manual.  See the first section of Chapter 8 "Analysis." 
  Groups are generic constructs that can be used at just about any stage of 
preparation, simulation, and analysis.  Custom groups are almost always required 
for analysis, except for the most trivial tasks.

-Justin

>
> 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
>>
>> ==================================================
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>> Gromacs Users mailing list
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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

==================================================