AMBER Archive (2007)

Subject: AMBER: Calculating cumulative average

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Thu Aug 02 2007 - 12:00:10 CDT

Who would be so kind to adapt the awk script below (from thermodynamic
integration tutorial A6)

BEGIN{ isd=0; epsum=0; npts=0 }

/Molecular dynamics:/{
    while( $1 != "nstlim") getline;
    split($3,a,",");
    nstlim = a[1];
}

/DV\/DL,/{ isd=1}

/NSTEP/{ if(isd == 1 ){nstep = $3 ; tim = $6; }}

/EPtot/ {
    if(isd == 1 ) {
        if( nstep >= nstart ) {
            npts += 1;
            eptot = $9;
            epsum = epsum + $9;
            print tim,eptot,epsum/npts ;
        }
        isd = 0;
    }
}

to get cumulative average for both PM3ESCF and EPtot for QM/MM (tutorial A2). I
should certainly learn the language for such scripts, though I am immediately
interested in the reliability of PM3ESCF in relation to nstlim#.

Thanks a lot

francesco pietra

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