VMD-L Mailing List

From: Bruno Luís Pinto de Oliveira (boliveira_at_itn.pt)
Date: Fri Oct 21 2011 - 12:37:34 CDT

Dear Pawel,

Thanks a lot your nice and clear explanation.It was something like this I was in need...

> The setup you describe is what you did in NAMD, but you visualize the results with VMD which is not aware of that setup.

> What you read into VMD is the topology (PSF file) and coordinates (for example, DCD file). If you read in
> just a PDB file, the topology is guessed so you
should read in both PSF and DCD to visualize the trajectory.
> Neither if these files contain any information of your FEP setup. In fact, due to technical limitations both of
> the forcefields used in NAMD, and of the VMD program, the topology of the system (number and types of
> atoms,bonds etc.) must be constant over the entire trajectory - both during simulation and visualization.

OK... tks

> What NAMD does during FEP simulations is that the both vanishing and appearing parts of the system are present and
> included in all calculations, but only the energy and force terms related to these parts are multiplied by your lambda parameter > or (1-lambda),
respectively.
> VMD has no knowledge of all this and it faithfully displays all atoms over the entire trajectory.

OK... tks

> Even with the core displayed all the way by VMD, the interactions with the vanishing part should get softer and softer so at
> the end of your simulation (where lambda=0) you should see that these atoms are not "felt" by the "arms" and you probably
> should see the "arms" (more) flexible and their or other atoms probably overlapping with the core.

That is what I was expecting...

> If not, it might indeed mean that something is wrong with your results. Note that FEP modeling is inherently intricate and the
> results are sensitive to the setup. As far as I remember, good equilibration and sampling (in terms of lambda steps) of the
> beginning
and the end of the transformation is especially important.

I know...!!! I am optimizing my lambda and simulation time for a quite long ... now the forward and the backward simulations are converging... At least for me it seems that things are not going so bad...

> Having said that, the best what you can do with VMD visualization is to mimic the transformation occuring over the
> trajectory.

> This is what I proposed in my previous email. Because VMD has no knowledge of the lambda parameter, you should write a > Tcl function which will calculate the lambda from the trajectory frame number (for example; or you can provide a file mapping > frame to lambda), and use this lambda to make the graphical representation of the core to vanish; for example, by scaling the > atom and bond radii by lambda, or by making the representation gradually more transparent.

Now everything it´s more clear for me... Now I am "guided"... I don´t have much experience in tcl script but I will search the forum, look for some tutorials and at the end I will find a solution... ;)

I ran a mailing list from beginning to end and could find any explanation or post related with what we are discussing...
Thanks a lot again...:)

Bruno

Regards