Front End for NAMD?
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. 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. Thank you. Sincerely yours, Rudy
Hi, I think every software has its strength and weakness. That is why we use them all in a complementary manner. And that is why we need them all. Regard, Andrei On Sun, Jan 6, 2013 at 5:47 PM, Rudy J. Richardson <rjrich@umich.edu> 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.
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.
Thank you.
Sincerely yours,
Rudy
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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
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
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... --Eric 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
participants (3)
-
Andrei Neamtu -
Eric Pettersen -
Rudy J. Richardson