[MMTK] MD with fixed atoms

Konrad Hinsen research at khinsen.fastmail.net
Fri May 6 05:57:04 UTC 2011

On 5 May 2011, at 23:18, Victor Muñoz wrote:

> Problem fixed. I just used the VelocityVerletIntegrator() instead of  
> writing it like in the MD integrator in python example. This way the  
> universe keeps updating and I can mantain fixed the atoms I want.

Now I understand what went wrong: every integrator and minizer has to  
know about fixed atoms and handle them specificlly.  
VelocityVerletIntegrator does, the Python example doesn't, because I  
wanted to keep it as simple as possible.

> Now I have other problem when I try to save the MD. When I run the  
> Trajectory() script in the MMTK, I get the error 'NoneType' object  
> has no attribute 'name' in :
> File "/home/victor/bin/chimera_1.5.2/lib/python2.7/site-packages/ 
> MMTK/ChemicalObjects.py", line 486, in _typeName
>     return self.type.name

Which script exactly are you running? And what is your system? The  
error message points to some problem with identifying some object in  
your universe.

> I'm trying to save the dynamics into the netCDF format using the  
> universe created by the UCSF chimera, as the dynamics already works.  
> But neither Conrad nor I knows which type do we need in order for  
> Trajectory() to work.

Can you check (and tell me) what "self.type" is when the crash  
happens? You can find out quickly using a debugger such as pdb.

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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