[AMBER-Developers] XMIN minimisation and coordinates

From: Ben Roberts <ben.roberts.geek.nz>
Date: Thu, 20 Jan 2011 16:59:08 -0500

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.

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Received on Thu Jan 20 2011 - 14:00:03 PST
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