AMBER Archive (2003)

Subject: Re: Superimposed trajectory

From: David A. Case (case_at_scripps.edu)
Date: Tue Jun 10 2003 - 09:53:42 CDT

On Tue, Jun 10, 2003, Filip Razga wrote:
>
> My problem : I want to do a trajectory , which every one snapshot is
> mass fitted to the first or reference snapshot, thats mean that the
> molecule will be superimposed every snapshot to the reference-by using
> Ptraj and create a superimposed trajectory without the rotation of the
> molecule.The trajectory will stored the coordinates of the fitted
> structure every time step-something like mass weight fitted rmsd, but
> without calculating the rmsd values, only stored the fitted coordinates.
>

The "rmsd" command in ptraj does what you describe above. You can ignore the
rmsd values if you wish, and just use the superimposed trajectory for
other analysis.

..hope this helps....dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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