[gmx-users] RMSD from the average structure

[Erik Marklund]

Average coordinates are problematic and not generally representative. Consider for instance the average coordinates of a methyl group connected to X. The rotation around the C-X bond causes the average positions of the hydrogens to line up. Consider using g_cluster to find representative structures from your trajectory.

Erik

On 26 Apr 2013, at 06:59, bipin singh <bipinelmat at gmail.com> wrote:

> Thanks for your reply.
> Actually I am interested to see how much structural deviation is occurring
> in a protein during the simulation from its average position of atoms
> rather than the initial position (crystal structure or starting structure).
> The motivation of doing this analysis is the fact that in real solution
> phase, a system may not be static and if we consider the time average
> structure of a simulation to be the real representative of the structure in
> solution phase rather than static crystal structure.
> 
> 
> 
> 
> 
> 
> 
> On Fri, Apr 26, 2013 at 2:06 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> 
>> Hi Bipin Singh,
>> 
>> That indeed gives you the RMSD against the average. Do think about it a bit
>> more: do you want the average of the whole structure, or should you account
>> for a phase of relaxation?
>> 
>> Cheers,
>> 
>> Tsjerk
>> 
>> 
>> On Wed, Apr 24, 2013 at 2:17 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> 
>>> 
>>> 
>>> On 4/24/13 3:06 AM, bipin singh wrote:
>>> 
>>>> Hi all,
>>>> 
>>>> Please let me know whether this is the right way to calculate RMSD from
>>>> the
>>>> average structure from a simulation:
>>>> 
>>>> g_rmsf -f traj.xtc -s average.pdb -od rmsdev.xvg
>>>> 
>>>> 
>>>> average.pdb: is the pdb file produced using -ox option of g_rmsf.
>>>> 
>>>> 
>>> You can calculate RMSD with respect to whatever structure you like, but
>>> the interpretation and justification for doing so are up to you.
>>> 
>>> -Justin
>>> 
>>> --
>>> ==============================**==========
>>> 
>>> Justin A. Lemkul, Ph.D.
>>> Research Scientist
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>> 
>>> ==============================**==========
>>> 
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>> 
>> --
>> Tsjerk A. Wassenaar, Ph.D.
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> 
> 
> 
> -- 
> *-----------------------
> Thanks and Regards,
> Bipin Singh*
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