[Chimera-users] Front End for NAMD?
pett at cgl.ucsf.edu
Mon Jan 7 17:30:31 PST 2013
There is one significant reason that having a direct interface to NAMD would be nice (rather than, or in addition to MMTK/OpenMM): the ability to more easily access MDFF for fitting structures into EM density maps. Whether that's enough to actually get us to do it...
On Jan 7, 2013, at 5:20 PM, Rudy J. Richardson wrote:
> Dear Eric,
> You and the Chimera team are welcome to the kudos. I think it is amazing what Chimera does for free that major companies are charging for.
> Regarding further development of Chimera as a GUI for NAMD, I really hope that someone might be persuaded to do this. As I said, I believe there is a real need for a new generation of MD interfaces that could open up the field. From what I have seen, I think it is possible that Chimera could provide an interface that is substantially better than anything currently available, and this would be a major contribution.
> In any event, thanks for the existing elegance of Chimera and keep up the good work.
> Best wishes,
> On Mon, 7 Jan 2013, Eric Pettersen wrote:
>> On Jan 6, 2013, at 7:47 AM, Rudy J. Richardson wrote:
>> To whom it may concern:
>> First, my profound thanks to the creators of Chimera for a
>> superb research and teaching tool. I am especially grateful for
>> the excellent interface with Modeller for doing such things as
>> creating and optimizing loops to repair chain breaks in X-ray
>> structures; this feature is greatly improved in v. 1.7rc.
>> Dear Rudy,
>> Thank you very much for the positive feedback. We put in a lot of effort to
>> make the 1.7 version of loop modeling more useful as well as easier to use,
>> and to make it more bulletproof in the face of exotic input structures.
>> It's gratifying to hear that it's appreciated.
>> I am also grateful that Chimera can be used to visualize results
>> of MD simulations with, e.g., NAMD. However, in addition to
>> viewing results, it would be great if Chimera could be developed
>> to serve as an interactive GUI for setting up, running, and
>> analyzing NAMD simulations, including steered MD, as well. There
>> is a real need to make MD more accessible to a wider range of
>> scientists, and it appears that Chimera could be an excellent
>> platform for this. I realize that VMD has co-evolved with NAMD
>> for this purpose, but VMD lacks the integration, polish, and
>> intuitive ease of use of Chimera.
>> Though we would love to provide this kind of interface, the reality is that
>> we are a small team of programmers and therefore we really have to focus on
>> additions and improvements that provide the most "value" to our user
>> community -- which really largely translates into mostly providing unique
>> features and capabilities not found in other packages, even if we might be
>> able to provide them "better". Also, it's quite difficult to propose to a
>> funding agency that you are going to provide something that another package
>> already provides, just a little bit better. :-) So in practical terms this
>> works out to the answer that Andrei already supplied -- you have to use the
>> best available tool for the job.
>> Nonetheless, there may be some related capabilities on the horizon. Victor
>> Munoz and J.D. Marechal are working on an interface to more of Chimera's
>> MMTK capabilities. Some initial fruit of this effort is the "Calculate
>> Normal Modes" tool included in the daily build. An interface to calculating
>> MMTK MD runs is being worked on. We are also thinking about including an
>> interface to OpenMM for running MD trajectories. That is still in a pretty
>> preliminary phase.
>> Eric Pettersen
>> UCSF Computer Graphics Lab
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