[gmx-users] Re: Calculate RMSD

Justin A. Lemkul jalemkul at vt.edu
Mon Apr 26 13:05:34 CEST 2010

Please keep all Gromacs-related correspondence on the gmx-users list.  I am not 
a private tutor, and you stand a much higher probability of receiving a useful 
response by contacting the community.  Further, discussions are archived so that 
others can benefit from the questions and answers.

Both commands are syntactically correct, they just measure RMSD based on 
different starting structures - the un-minimized structure held in em.tpr 
(usually a crystal structure or something) and the structure that has been 
(presumably) minimized and equilibrated in some way.  The difference between the 
two is likely small, but that will depend on how you've treated the system prior 
to running MD.  The proper use of the command depends on what you want to do. 
If you want RMSD relative to the crystal structure, use the first invocation of 
g_rms.  If you want RMSD relative to the minimized, equilibrated structure, use 
the second.


lena farnandis wrote:
> Dear sir,
>          When i wish to calculate RMSD of protein using *g_rms* command 
> which file i should use to calculate it to get proper evaluation
> two command is in tutorial are as follows.
> *g_rms  -s em.tpr  -f  md.trr -o rmsd.xvg*
> *g_rms  -f md.tpr  -s md.trr -o rmsd.xvg
> *which is correct both command shows different RMSD.
> please help me or clarify its use.
> waiting for your reply
> Research student,
> *


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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