Re: [AMBER-Developers] XMIN minimisation and coordinates

From: <istvan.kolossvary.hu>
Date: Wed, 23 Feb 2011 19:10:40 +0100

Ben,

A couple of things that come to mind. Could you run the same molecule
with AmberTools? If it's OK there it might be an indication that the
interface to Sander has recently been broken. The other thing is to
turn on XMIN verbosity. That way you would have energy and gradient
RMS printout from inside XMIN and those number should be the same as
in Sander since the same energetic routines compute them. Actually,
when you say you see this big discrepancy at the very first step, I
wonder if Sander output is simply out of sync and reports the energy
before any minimization steps took place.

    Istvan

Quoting Ben Roberts <ben.roberts.geek.nz>:

> Hi Istvan,
>
> On 21/1/2011, at 4:09 a.m., istvan.kolossvary.hu wrote:
>
>> Hi, Ben, Jason,
>>
>> Indexing shouldn't matter since I am simply pasting values in a memory
>> location given to me and it should be irrelevant how that location is
>> indexed. I am really puzzled what can be wrong since XMIN returns
>> coordiantes every time it needs a gradient and if those coordinates
>> were incorrect XMIN would fail spectaculary in teh first place. Ben,
>> where do you fetch XMIN coordinates? One has to be careful, because
>> XMIN works in a totally different environment internally. When
>> coordiantes are returned XMIN makes sure that their serial numbers
>> correspond to those used externally. This has to do with frozen atoms.
>> If there are no frozen atoms XMIN internal arrays should exactly
>> correspond to the corresponding external arrays. One good test would
>> be to check if the same behavior happens with a totally flexible
>> system. Another thing is that the only way XMIN knows about a frozen
>> atom is when all three corresponding gradient values are exactly zero
>> (checked by ==0.0). I am not familiar with Sander at all, if there has
>> been any changes in marking frozen atoms, XMIN will fail. Hope this
>> helps. If you can give me a concrete example I can check it out, but I
>> have only used AmberTools, never Sander.
>
> This afternoon I did a bit more testing on this. I use the
> coordinates array, which in Sander is passed into run_xmin (in
> lmod.f). There, it's used in two places: a call to xminc and another
> call to gradient_calc (which then calls force). After that, the next
> places the coordinates array is used are the calls to write restart
> and trajectory files.
>
> I tried with a totally flexible ethane molecule in vacuum (no PBC,
> etc). The same problem was observed, with the coordinates at the
> first step corresponding to a much higher energy than that reported
> in the log file. I'll see if I can pinpoint which subroutine is
> confused - whether it's xmin or gradient_calc.
>
> Cheers,
> Ben
>
> --
> For greater security, I support S/MIME encryption.
>
>




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Received on Wed Feb 23 2011 - 10:30:05 PST
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