the first thing to consider in this kind of circumstance is whether you have
ever seen such an application reported in the literature, or if just
exploring the method itself will be a research project. if you have similar
papers, then they will guide you until you reach technical problems, at
which point you might post them here. If there is no previous example in the
literature, perhaps the best approach is to try it out and see what happens,
and if you run into technical problems post them here.
almost certainly, minimization will not do what you need. TMD for large
structure changes should be considered a very advanced method to be
undertaken after you are very familiar with normal MD simulations, then the
TMS will be a step up from those. right now your question needs to be a
little more specific about your goals and current knowledge and then we can
try to help with the technical questions (but it is very hard to ask in
email for someone to give a full explanation of how to do something
complicated).
good luck
On Tue, Feb 10, 2009 at 12:36 PM, balaji nagarajan <balaji_sethu.hotmail.com
> wrote:
>
> Dear Amber,
>
>
>
>
>
>
>
>
>
> I would like to do Targeted Molecular
> Dynamics for DNA .
> I am having the crystal structure of
> two different DNA structures
>
> from the same sequence among them one
> is a junction
>
> the all atom RMSD between the two is
> 14.54.
>
> among this two i kept one as a
> referance coordinate.is it possible to do TMD with such a huge RMSD
> difference ,
> I saw the test case given in the package
> i could not under stand the minimization procedure
> can any one suggest me how minimization to be carried out .thanks in
> advance
> balajiUOM
>
>
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Received on Wed Feb 11 2009 - 01:20:43 PST
