AW: NAMD Question: Generating ensemble of structures

From: Norman Geist (
Date: Wed Aug 31 2016 - 01:29:49 CDT

Hi Oscar,


while NAMD can’t explicitly write PDB trajectories (series of coordinates), the resulting DCD files can easily be converted using e.g. VMD and a small TCL script (or even the GUI for only 10 structures). Also NAMD is able to write PDB format coordinates files at the end of a simulation (usually used as restart for continuing runs (needs “binaryoutput no”).


Btw, if you want to perform MD on a protein, you might be interested in the new QwikMD plugin available in vmd-1.9.3b1, since it helps you setting up simulations via GUI and run it directly out of VMD. (You’d just need to install a SMP version of namd, easily downloadable and precompiled). Additionally such a superimposition you mentioned can be done also in VMD very easy, using the “RMSD Trajectory Tool”



Von: [] Im Auftrag von Oscar Bastidas
Gesendet: Mittwoch, 31. August 2016 07:52
Betreff: namd-l: NAMD Question: Generating ensemble of structures




I am a novice at using NAMD and I have a question on whether the NAMD software can be implemented to provide as output PDB structures at regular intervals (specified by me in accordance with my total running simulation time) such that I end up with an ensemble of structures similar to the ensembles provided by protein NMR structure elucidation studies. I am interested in knowing, if this is possible with NAMD, how it would be implemented. Would you please tell me if to your knowledge this is a possibility with NAMD and how I would go about to do it?


If this is not a possibility, then I am open to the following alternative, again, if it is possible: Can I have NAMD produce a final PDB structure at the end of a simulation for a certain amount of time and, then, once that simulation is finished, feed this output PDB structure that shows the final trajectory stopping point as the input PDB into another separate simulation run? As you might imagine, I'd intend on repeating this multiple times (I'm specifically interested in obtaining an ensemble of 10 structures) to obtain superimposable structures that would ultimately resemble the aforementioned NMR ensemble, but show the actual range of true motion of the protein (like strobe photography of a golfer). Thank you for any help you can provide.


Respectfully submitted,


Oscar B.

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