you could do this many ways- impose a restraint on the backbone, use heat,
and so on. It's hard to say more without knowing what exactly you are trying
to achieve.
On Tue, May 31, 2011 at 10:06 AM, Daniel Schaal <
daniel.schaal.uni-bayreuth.de> wrote:
> Dear all,
>
>
> i am running am MD in explicit solvent and want to manipulate the
> conformations of my peptide at a certain point of time.
> This should look like a sudden but small extension of the back bone in
> order to find to the energetic minimum again. Is this possible in general
> and without blowing up my system?
> I think the main problem would be the negligence of the additional
> (necessary?) minimization, or is this not the case.
> For example can this be done by increasing the temperature for a short time
> and then going back to the initial ?
>
> Thanks in advance for every response.
>
>
> Daniel Schaal
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Received on Tue May 31 2011 - 11:30:02 PDT
