Thanks Dr. Case. Between yesterday and now, I ran another very short
calculation this time over 10ps (I checked the MD trajectory i.e. rmsd of
c-alpha atoms of the entire system to make sure it is quite stable over
those chosen 10ps) and got different results. This time around the complex
and receptor both have a huge STD and even larger. I find this very strange
since I chose to generate 6 snapshots in those 10ps, given the small
timeframe and the equilibration state, I would think that the energies
should be very similar w.r.t each snapshot and would not produce such a high
STD. I looked at the structure in vmd and nothing looks weird
post-simulation, hence I doubt if there is an outlier. Would you recommend
running the Nmode calculations over individual snapshots, say run 5
different individual calculations over 5 separate snapshots and manually
calculate the STD from it? But, again it would be nice if I could figure out
this discrepancy.
# COMPLEX RECEPTOR LIGAND
# ----------------------- -----------------------
-----------------------
# MEAN STD MEAN STD
MEAN STD
# ======================= =======================
=======================
TSTRA 17.47 0.00 17.46 0.00 13.89
0.00
TSROT 17.84 0.01 17.82 0.00 12.01
0.01
TSVIB 2762.57 19.67 2719.56 19.89 48.03
3.15
TSTOT 2797.88 19.67 2754.84 19.90 73.94
3.14
# DELTA
# -----------------------
# MEAN STD
# =======================
TSTRA -13.87 0.00
TSROT -11.99 0.01
TSVIB -5.02 22.45
TSTOT -30.89 22.45
Any views on what might have caused the change of output this time?
Thanks
-Rima
On 2/16/07, David A. Case <case.scripps.edu> wrote:
>
> On Fri, Feb 16, 2007, Rima Chaudhuri wrote:
>
> > # MEAN STD MEAN
> STD MEAN STD
> > TSVIB 2753.67 2.69 2739.67 18.12 34.60
> 0.52
>
> It is indeed odd that the standard deviation for the receptor is so much
> larger than for the complex. You will probably have to study the
> individual
> nmode outputs to try to figure out why -- is there one "oddball" outlier
> that
> is greatly influencing the standard deviation? etc.
>
> ...good luck...dac
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
--
-Rima
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Feb 18 2007 - 06:07:52 PST
