AMBER Archive (2006)

Subject: AMBER: rbornstat average and fluctuations incorrect when nrespa != nrespai

From: Ingvar Lagerstedt (
Date: Fri Oct 20 2006 - 11:17:08 CDT

I think I have found a bug for the rbornstat option when nrespa !=
nrespai. I noticed that I got NaN's for the fluctuations and that the
averages was sligthly off in some cases, including the gb_mb test case.
Rerunning with fewer steps and the average can become large than the max
value. I traced the problem to that the value of tspan matched the
nrespa setting rather than the nrespai setting when writing the summary
statistics in runmd.f

The following is a suggested fix:

diff runmd.f.Amber9 runmd.f
< integer nvalid

 >    integer nvalid, nvalidi
 >    nvalidi = 0
 >    ! added for rbornstat
 >    if (mod(irespa,nrespai) == 0 .or. irespa < 2) nvalidi = nvalidi + 1
 >          ! Born radii stats collected every nrespai step not nrespa step
 >          tspan = nvalidi

-- Ingvar Lagerstedt, Scientist ClearSpeed Technology plc, Tel: +44 117 317 2055, Fax: +44 117 317 2002

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