[gmx-users] g_rmsf fitting

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Jan 3 16:41:18 CET 2008

Hi Tang,

It's just the general case of least-squares fitting:

1. Bring centres of geometry/mass to origin
2. Calculate (mass-weighted) rotation matrix
3. Rotate structure
(4. Calculate squared displacements)

But what do you mean with 'very different'. Can you provide an example? What
command line did you use? Do you have multiple subunits and have jumps over
PBC between the two reference structures?



On Jan 3, 2008 3:37 PM, tangxuan <tangxuan82 at gmail.com> wrote:

> Hi,
> Does anyone know how  fitting step works in detail when running g_rmsf?
> When I used two different tpr files with same protein structure but
> different atoms position, the result is very different.
> Can you explain this ?
> many thanks!
> Tang
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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