Re: how to visualize an alchemical FEP transformation??

From: Axel Kohlmeyer (
Date: Sat Oct 22 2011 - 11:33:47 CDT

> I still don´t understande how it is possible to prepared a Figure, for example, like this:
> I ran  the VMD and NAMD mailing lists (manuals also) from the beginning to the end and could not find any post related with this subject.
> Do you have any idea??

very simple, you only show what you want to show.
VMD has a selection language that lets you determine
to great detail of what is shown. if you believe that any
picture that you see posted and published is showing
you the plain data without any manipulation, then you
have to learn a _lot_.

other than that, i have to remark that given VMD's
graphical capabilities, those are particularly ugly
visualizations that are not very well done in showing
what they want to show...


Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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