[Chimera-users] Front End for NAMD?

Eric Pettersen pett at cgl.ucsf.edu
Mon Jan 7 17:30:31 PST 2013

Dear Rudy,
	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,
> Rudy
> 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
>>                         Eric Pettersen
>>                         UCSF Computer Graphics Lab
>>                         http://www.cgl.ucsf.edu

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