Re: [AMBER-Developers] XMIN minimisation and coordinates

From: Ben Roberts <>
Date: Tue, 1 Mar 2011 16:40:46 -0500

Hi Istvan,

> Thanks, I'll have a play.
> But I think I may have stumbled across something relevant. Specifically, if I ask sander for only one cycle of minimisation, I get good coordinates in both "restrt" and "restrt_1". If I ask for two cycles, "restrt_1" (that is, the coordinates after only one step) is broken, and sander exits with this message:
> Error opening unit 17: File "restrt_1" exists and may not be overwritten
> (I've changed this message in my development version to improve its clarity, so you won't be able to grep for it, but it's what's thrown by amopen() if a file already exists that it's trying to write to.)
> So it seems that something is happening after the fact to mess up coordinates. I'll do further investigation.

OK, so I've found out a bit more about what's going on:

In sander, the coordinates are only written out (to restart files or trajectories) if the return_flag value from xminC is 4, 5 or 6. But the "correct" coordinates (i.e., those reported if I do only a single step of minimisation in sander or in NAB) are those obtained if the return_flag value from xminC is 7, 8 or 9 (which, needless to say, I get after a different pass through xminC).

In the tests I've so far managed to do, a return_flag value of 1, 2 or 3 is not obtained, nor is zero (I haven't allowed enough steps for convergence to be reached).

Thus, my question is: what values of return_flag actually correspond to a "real" minimisation step of the sort that can be written out to restart / checkpoint files? Or is this a meaningless question in the context of xmin? I thought, when I asked this earlier, that I received an answer of 4, 5 or 6; but the numbers I'm seeing today call that into question.

Or, put another way: under what conditions are the lines starting "MIN:" printed out (assuming the appropriate verbosity is turned on)? And are those same conditions available to the parent routines, whether xmin (in NAB) or run_xmin (in sander)? Because I want to be able to save the coordinates at those same points.


For greater security, I support S/MIME encryption.

AMBER-Developers mailing list

Received on Tue Mar 01 2011 - 14:00:02 PST
Custom Search