[gmx-users] Questions about g_sham

[Warren Gallin]

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
> 
>