AMBER Archive (2007)

Subject: Re: AMBER: NAB MD Output

From: Andreas Svrcek-Seiler (svrci_at_tbi.univie.ac.at)
Date: Tue May 08 2007 - 05:09:18 CDT

Hi,
>
> I get something like this in my output:
> iter Total bad vdW elect. cons. genBorn frms
> ff: 0 -1254.79 391.88 -30.05 807.69 0.00 -2424.30 9.22e+00
> md: 1 0.001 60.31 -1264.87 -1204.56 79.35
>
Only adding to Russ' explanation: "cons." is the constraint (rather
restraint ?) energy. Unless your wcons (constraint weight ?) is larger
than zero *and* ans some atoms are set to be restrined to specific
positions, this will give 0.0.

To separate "md" from "ff" output (e.g. to generate pretty curves),
you might grep for ^md: or ^ff: in your logfile.

If you hav a log-file containing lines like above (say md.log)
grep ^md: md.log
will give you just
md: 1 0.001 60.31 -1264.87 -1204.56 79.35
and ^md: md.log |awk '{print $3,$7}' |xmgrace -pipe
would give you the temperature as a funtion of time (in picoseconds)
and show it as a curve in xmgrace.

good luck
Andreas

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