[MMTK] pMoldyn scripting problems

Konrad Hinsen hinsen at cnrs-orleans.fr
Thu Aug 17 15:50:42 CEST 2006

On Aug 16, 2006, at 17:20, ALEJANDRO MAXIMILIAN SUAREZ wrote:

> I'm not sure if this is the correct mailing list for a problem like  
> this,
> however it seems some of your have worked on both codes. Please  
> disgregard this
> if it is not a relevent topic.

This list is as good a place as any for such questions...

> However, I am running into a few problems finding documentation on  
> constructing
> pMoldyn scripts. I am having trouble in extracting units from the  
> nc files that
> are produced (ncdump shows no units for frequency or Q). Looking  
> through the

After a quick check of nMOLDYN-generated files on my disk, it seems  
that nMOLDYN does not create unit attributes for its output files.

> nMoldyn source I haven't been able to find the "units_q" variable  
> that is set
> within the xMoldyn GUI when preparing a simulation. I haven't been  
> able to sift
> through it all too well as I am relatively new at Python, but I  
> also am at a
> loss as to why the frequency units are not being set as well.

There are units_length and units_frequency as well.

> I have been using the default input file generated by xMoldyn as a  
> stepping stone to figuring out these problems, but can not find any  
> other documentation on how to construct these input files other  
> than some small examples.

There isn't much documentation yet, unfortunately. It is being worked  
on, but won't be ready very soon.

> My second issue arises from filtering the data so I see the  
> contribution of only
> certain specific atoms to the spectra, however I feel it more  
> pertinent to get
> accurate scale on my data before specifying more complicated  
> specifications.

Unless you explicitly specify different units, the default units are:

- nm for lengths
- 1/nm for wave vectors
- 1/ps for frequencies

These are in fact the default units of MMTK.

As for atom selections, there are three approaches:

1) Use the atom selection dialog in xMoldyn. This is the easiest  
solution, but it is limited to the predefined selections.

2) Write a Python function that returns the selected atoms as an MMTK  
object (usually a collection). The function must be called  
atoms_code, and the line starting with "atoms=" must be removed from  
the input file. I should have an example for this somewhere, but I  
cannot access my compute machines at the moment...

3) Mark the atoms to be selected in a hand-edited PDB file. I just  
know that this option exists, but I don't know how it works precisely.

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: hinsen at cnrs-orleans.fr

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