[MMTK] Using MMTK

khinsen at cea.fr khinsen at cea.fr
Mon Jul 18 21:28:43 CEST 2005


On 18.07.2005, at 18:33, Matias Saavedra wrote:

> But, as time is my principal concern, can i use a
> minimized pdb structure to launch again the
> minimization, expecting a BIG reduction in calculating
> time, compared with the very first minimization?

No. A reduction, yes, but not a big one. The slowest part of  
minimization for normal modes is the final one, which goes to high  
precision. All of that is lost when you use PDB files.

However, it is possible to do whatever you do to PDB files to in-memory  
configurations. There is some code for mutating residues (used  
internally for cysteins), but there is also the possibility of building  
a representation of the new chain and then copy over the positions from  
the previous one atom by atom.

Konrad.
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Konrad Hinsen
Laboratoire Leon Brillouin, CEA Saclay,
91191 Gif-sur-Yvette Cedex, France
Tel.: +33-1 69 08 79 25
Fax: +33-1 69 08 82 61
E-Mail: khinsen at cea.fr
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