[gmx-users] reg g_morph

[Justin A. Lemkul]

vidhya sankar wrote:
> Dear Justin,
>                    Thank you for your patience reply.
> When i use g_morph i have got rms-interm.xvg  file. the second and third 
> colum of this represents what value. i am not able to understand this

Read the headers of the .xvg file.  Presumably it is RMSD.

> Also With reference to what structure the rmsd  is calculated

g_morph -h:

"Finally the RMSD with respect to both input structures can be computed if
explicitly selected (-or option). In that case an index file may be read to
select what group RMS is computed from."

The RMSD is relative to whatever group you told g_morph to use.

-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

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