Justin,
Yes, in order to use the implemented free energy method, the end-to-end
distance has to be treated like a constraint, creating a closed ring of
constraints, which on some rare occasions leads to an instability and the
system blows up.
I think that my best move is to write a little script that creates a
free energy landscape for 1 dimension only. Now that I've got g_sham figured
out, this simple case should be straightforward (he said, invoking the wrath of
the gods).
Thanks for your insight.
Warren
On 2010-06-23, at 12:03 PM, Justin A. Lemkul wrote:
> Warren Gallin wrote:
>> OK, what if I have only one dimension (end-to-end distance), is there any
>> way to do that in GROMACS, or is the best way to just write a little app for
>> myself?
>
> Sounds to me like a problem for PMF, but I seem to recall you had some issues
> with that. g_sham requires 2 dimensions, so you can't use it for your
> purposes.
>
> -Justin
>
>
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