[gmx-users] RMSD from the average structure

[Tsjerk Wassenaar]

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>
>
> ==============================**==========
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>



-- 
Tsjerk A. Wassenaar, Ph.D.