Hi Matt,
amber does not report dvdl values if they are exactly zero. Depending on
your system, this might happen for some lambda values and is not
neccesarily an error.
Also if you run the same molecule with two different charges, not only
will your dvdl be different but also your trajectory will change.
Regards,
Thomas
Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA
On Thu, 8 Nov 2007, Cooper, Matthew wrote:
> Hi,
>
> I am experiencing difficulties with thermodynamic integration in Amber
> 9.
>
> I use the same input deck for numerous integrations. Occasionally, there
> will be no data for DV/DL, though a summary will be printed that
> contains only zeros.
>
> Rerunning the script will sometimes result in DV/DL averages being
> calculated though not always. If I run two molecules with identical
> starting positions but different charges, one may fail while the other
> will not.
>
> Does anyone have any experience with this?
>
> David wrote a while ago, in response to a similar question:
>
> <<Are you sure that the two Hamiltonians are really different? Try a
> one-step
> run with clambda=0, and with clambda=1 to make sure you are really
> getting
> different energies. (The behavior you report, not geting DV/DL at each
> step, but still getting a summary, with all values zero, is consistent
> with not having any energy difference between the two Hamiltonians.)>>
>
> I have checked - the energies are different at clambda = 0 and clambda =
> 1, at least according to the average after 1250 steps.
>
> Thanks,
>
> Matt
>
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Received on Wed Nov 14 2007 - 06:07:47 PST
