[gmx-users] reg g_morph

Justin A. Lemkul jalemkul at vt.edu
Sat Jul 2 18:24:23 CEST 2011

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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