[gmx-users] rmsd between different monomers

[Justin A. Lemkul]

Anupam Nath Jha wrote:
>>
>> Anupam Nath Jha wrote:
>>> Dear all
>>>
>>> I made an index file with 4 different groups for 4 different chains (since my
>>> protein is a tetramer) and then run
>>>
>>> g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out
>>>
>>> to get the rmsd between two different monomers from the same structure,
>>> it asked me two different groups and I gave 0 and 1.
>>>
>>> The output file is like this
>>>
>>> # g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o New
>>> #
>>> # g_rms is part of G R O M A C S:
>>> #
>>> # Grunge ROck MAChoS
>>> #
>>> @    title "RMSD"
>>> @    xaxis  label "Time (ps)"
>>> @    yaxis  label "RMSD (nm)"
>>> @TYPE xy
>>> @ subtitle "C-alpha_chain2 after lsq fit to C-alpha_chain1"
>>>    0.0000000    0.0000001
>>>
>> In the command you've given (with the same file for -s and -f), you're computing
>> the RMSD at time zero, after fitting to the structure at time zero, so the RMSD
>> must be zero.
> 
> 
> but I am giving different groups (as chains). I am trying to get RMSD between
> two monomers in same structure so what's wrong in that....
> 

It doesn't matter.  The structure for calculation (-f) and the reference 
structure (-s) are identical, so the RMSD has to be zero, regardless of the 
fitting group and calculation groups chosen.

-Justin

> -
> anupam
> 
>>> so the rmsd = 0.0000001
>>>
>>> whereas when I use online server it gives me 1.4.
>>>
>>> so what am I doing wrong?
>>>
>> Then whatever you're giving the online server is different.  The Gromacs
>> calculation seems to be correct.
>>
>> -Justin
>>
> 
> 
> 
>>> regrads
>>> anupam
>>>
>>>
>>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
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> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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