Re: [AMBER-Developers] XMIN minimisation and coordinates

From: Jason Swails <>
Date: Thu, 20 Jan 2011 17:55:17 -0500

xmin is written in C, correct? Could it be that array indexing may be an
issue (C indexes from 0 whereas Fortran starts from 1)? Naive suggestion
based on no code study whatsoever. Hopefully it's the issue, since it's
easy to fix (and potentially explains the described effects).

Feel free to deposit this email in the nearest receptacle (and luckily for
the environment it's not written on paper).

All the best,

On Thu, Jan 20, 2011 at 4:59 PM, Ben Roberts <> wrote:

> Hi all,
> People may recall that some months ago I added functionality to lmod.f to
> write out the coordinates (as restart files and/or as trajectory files)
> during an XMIN minimisation. However, recently I've come across a rather
> strange problem with the coordinates that are written.
> Specifically, the energy reported doesn't match the energy calculated from
> the coordinates. The written-out coordinates involve massively stretched
> bonds, while the energy calculation must have bonds at or near the reference
> length. If I freeze all but two atoms in a particular system using a
> bellymask, and compute the resulting bond energy, Amber reports a bond
> energy of 0.3128 kcal/mol, while the bond energy computed from the
> coordinates is 8.8964 kcal/mol.
> In a similar development, an attempt to minimise a structure with PUPIL
> will see pairs of link atoms fly further and further apart until they're too
> far apart for a link to be established. This is partly a PUPIL "feature" and
> may be changed. However - and here I display my ignorance of the XMIN
> algorithm - it seems to me that XMIN *may* be returning the "wrong"
> coordinates to the rest of sander.
> Is anyone able to advise on what might be happening here, and in particular
> why the coordinates are so different from what I might be expecting, so I
> can work out how to fix it if appropriate? Especially, I'd like to know
> whether this is expected behaviour for the XMIN algorithm. If it is, I just
> need to sort PUPIL out; if not, we need to sort other things out too, I
> guess.
> Cheers,
> Ben
> --
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Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER-Developers mailing list
Received on Thu Jan 20 2011 - 15:00:07 PST
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