[Chimera-users] some questions about new features, in particular MD

Eric Pettersen pett at cgl.ucsf.edu
Sat Aug 24 15:29:00 PDT 2013

Hi Lionel,

On Aug 23, 2013, at 12:50 AM, Lionel Nauton wrote:

> Hello
> I was very pleasantly surprised to discover a molecular dynamics module in the latest version of chimera, I used already "MD movie" to see the dynamics with NAMD made​​, but the ability to make dynamic from chimera is a real plus, thank you for that.

That interface is still very much in a preliminary stage, which is why it is only in the daily builds.  We are continuing to refine it in collaboration with the authors (Jean-Didier Marechal and Victor Munoz at the Universitat Autonoma de Barcelona) and hope to include it in an official release when we feel its ready.  You may have noticed there's no documentation yet. :-)

> in spite of this, one thing I do not understand why the minimization phase is parallelizedin the dynamics module and is not in standard mode, is a planned evolution, I'm too impatient?

While you are correct that the MD computation interface explicitly allows you to set the number of processors to use, for energy minimization if you are not on Windows and know enough about Unix command lines to set environment variables, you can set the MMTK_ENERGY_THREADS environment variable to the number of processors to use before running Chimera.  See these mailing list messages:

[Chimera-users] Parallel run
[Chimera-users] Need help for using Chimera

> Second, in the latest version (21-08-2013), I can not read trajectories files from GROMACS , I saturate the RAM (16 GB and 7 GB swap) and the program exits.the same dynamics made with NAMD in .dcd formatworks well, any idea ?

Since I now use the XTC Library to read Gromacs .xtc and .trr files, the entirety of the trajectory does get read into memory at startup, whereas for DCD files that is not the case -- the coordinates are read in as needed.  I'm guessing we're talking about a very large trajectory file?  The memory used should be roughly (8 x #atoms x #frames) bytes.  If you do the math for your trajectory and it comes out to much less than 16GB, please let me know and I will investigate.  The only alternative I can think of is to split your trajectory coordinates into more manageable chunks.


	Eric Pettersen
	UCSF Computer Graphics Lab
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