thank you sir
On Tue, Sep 10, 2013 at 8:18 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Mon, Sep 9, 2013 at 6:55 PM, Mary Varughese <maryvj1985.gmail.com>
> wrote:
> > thus is there two rms?
>
> The 'rms' and 'atomicfluct' commands are two different calculations.
> RMSD measures the deviation of the coordinates in a target frame to
> corresponding coordinates in a reference frame (i.e. how different is
> target from reference in Cartesian space), while atomic fluctuations
> measure the deviation of those coordinates over all frames. The reason
> one typically performs an RMS best-fit prior to calculating an average
> structure or atomic fluctuations is to remove overall translational
> and rotational motions that will otherwise be present.
>
> > also is it mass weighted backbone rms fit or just rms first mass :1-20?
>
> That's up to you. Typically performing an RMS-fit to an averaged
> structure results in less global motion compared to fitting to the
> first frame. You could also try rms fitting each frame to the previous
> one ('rms previous').
>
> -Dan
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Sep 09 2013 - 21:30:02 PDT
