[MMTK] Distance atoms, trajectory, and current configuration

Konrad Hinsen research at khinsen.fastmail.net
Wed Feb 10 19:45:58 UTC 2010

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> From: mmtk-bounces at starship.python.net
> Date: 10 February 2010 14:26:25 CEST
> To: mmtk-owner at starship.python.net
> Subject: Auto-discard notification
> The attached message has been automatically discarded.
> From: acevedo at mpi-muelheim.mpg.de
> Date: 10 February 2010 13:52:53 CEST
> To: mmtk at starship.python.net
> Subject: Distance atoms, trajectory, and current configuration
> Hi all:
> I´m really new using this programm, and I have gotten stuck with some
> issues. Basically, I would like to get some datas from a Desmond
> trajectory file. I was able to export this trajectory to a DCD format
> using VMD, and after correction of format using catdcd3.0 I could  
> get the
> nc version of my trajectory. The time variables of this trajectory  
> showed
> only 0s, and I do not know if this would be a problem with some MMTK
> applications later on.
>   The problem appeared when I tried to get distance values between two
> atoms along the trajectory. The kind of sequences that I´ve been using
> are the following:
> trajectory = Trajectory(None, 'Trajectory.nc')
> universe = trajectory.universe
> for step in trajectory:
>    d = step['configuration']
>    universe.setConfiguration(d) # to update the current configuration
>    universe.distance(atom1, atom2) # two atoms being part of a  
> covalent
> bond in the backbone, e.g. Ala4.peptide.N and Lys3.peptide.C
> This instruction gave me the same value for every step, about 0.13 nm,
> which is the expected value for this covalent bond. It seems that no
> configuration updating was posible and the value correspond to a  
> unique
> configuration (the first current configuration probably)
> Then I tried some modification of the same:
> for configuration in trajectory.configuration:
>    universe.distance(atom1, atom2, configuration)
> This gave me different values of distance for every step. The values  
> were
> about 0.5 nm, quite far from the expected 0.13.
> other forms such as: (atom1.position()-atom2.position()).length() were
> still giving values of about 0.5 nm.
> I don't know if I've missed something, but I proved the same procedure
> creating infiniteUniverse and CubicPeriodicUniverse when I imported  
> the
> DCD trajectory into a nc format.
> If somebody can help me solving the problem, it would be great
> Thanks
> Pablo
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