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
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Received on Mon Feb 21 2011 - 17:30:02 PST
