Hi,
I believe the RMS reported in LMOD is of all atoms to the central
(initial) structure.
-Dan
On Tue, Dec 11, 2012 at 12:37 PM, Wong, Sergio E. <wong105.llnl.gov> wrote:
> Dear Amber Users;
>
>
> I have a question about LMOD output in amber 10. Is the RMSD reported (see example below) based on all atoms or heavy atoms? Also, is it calculated using the starting structure as the reference?
>
> ________________________________________________________________
> Low-Mode Simulation
> ---------------------------------------------------------------------------
> 1 E = -118.117 ( 0.054) Rg = 5.440
> 1 / 6 E = -89.2057 ( 0.090) Rg = 2.625 rmsd= 8.240 p= 0.0000
> 1 / 8 E = -51.682 ( 0.097) Rg = 5.399 rmsd= 8.217 p= 0.0000
> 3 /12 E = -120.978 ( 0.091) Rg = 3.410 rmsd= 7.248 p= 1.0000
> 3 /10 E = -106.292 ( 0.099) Rg = 5.916 rmsd= 4.829 p= 0.0004
> 4 / 6 E = -106.788 ( 0.095) Rg = 4.802 rmsd= 3.391 p= 0.0005
> 4 / 3 E = -111.501 ( 0.097) Rg = 5.238 rmsd= 2.553 p= 0.0121
>
>
> Thanks;
>
> -Sergio
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--
-------------------------
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
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Received on Wed Dec 12 2012 - 11:00:01 PST
