[MMTK] Distance atoms, trajectory, and current configuration

Konrad Hinsen research at khinsen.fastmail.net
Thu Feb 11 07:35:08 UTC 2010


>> 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

That looks fine.

>> 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)

Unless you have a simulation with bond-length constraints.

>> 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.

Is that a periodic universe? In that case, perhaps something went  
wrong during conversion, resulting in invalid box sizes.

You can check the box parameters using

	print universe.basisVectors()

Konrad.
--
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Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research at  khinsen dot fastmail dot net
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