[gmx-users] g_rmsf fitting
tsjerkw at gmail.com
Thu Jan 3 16:41:18 CET 2008
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:
> 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!
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
3584 CH Utrecht
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users