[gmx-developers] dynamic topology
spoel at xray.bmc.uu.se
Sat Oct 25 10:40:52 CEST 2003
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.
> 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
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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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