[gmx-developers] dynamic topology

[David]

On Sat, 2003-10-25 at 00:18, Jason DeJoannis wrote:
> Hi All,
> 
>  I have a system full of Argon and Krypton atoms. During
> the simulation I pick some atoms and change their type.
> Or at least I try to change their type. So far I am changing
> a couple of things inside top->atoms such as the mass and 
> the type.
> 
>  Unfortunately this is not enough. The md trajectory is 
> identical to the reference simulation with no mutations.
> What else do I need to change? 
> 
>  I noticed that the force() routine does not use top->atoms 
> and therefore it might be necessary to change the mdatoms 
> data. Anything I am missing?

yes, for efficiency everything is copied from structures into long
array, gathered in mdatoms. Those are the ones you need to copy.
> 
> Thanks,
> 
> ---
> Jason de Joannis, Ph.D.
> Chemistry Department, Emory University
> 1515 Pierce Dr. NE, Atlanta, GA 30322
> Phone: (404) 712-2983
> Email: jdejoan at emory.edu
> http://userwww.service.emory.edu/~jdejoan
> 
> 
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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