[gmx-users] The RMSD of a metal ion

[Justin A. Lemkul]

simon sham wrote:
> Hi,
> I would like to look at the positions of a metal ion in MD relative to 
> its original crystal position. I tried g_rms, and I got the following 
> message:
> 
> "Fatal error :
> Need >= 3 points to fit"
> 
> Did I use the correct command to achieve this task?
> 

Generally, when one receives a fatal error, the answer is no :)

To do least-squares fitting, as the error says, three points are needed.  In 
your case, I suspect you have chosen the metal ion as the fitting and 
calculation group, so there is only one point in space to which fitting can be 
applied.  Even if g_rms ran, it would give you a zero RMSD, as fitting would 
always align the single ion with itself.

You will have to either fit to some other suitable reference group such that the 
RMSD of the metal ion is calculated relative to it, or do a rotational and 
translational fit of the trajectory with trjconv and issue g_rms -nofit to 
calculate the RMSD of the metal ion.

-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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