[gmx-developers] dynamic topology
jdejoan at emory.edu
Mon Oct 27 23:13:38 CET 2003
Good, that worked. In fact I took advantage of
the *mdatoms=atoms2md() to copy top->atoms to mdatoms.
It would be more efficient to copy only the atoms that
change but I am not worried about that right now.
Do you have any remarks about a more complex topology
change? For example, what if I wanted to simulate mutation
in an O2/Argon mixture (I'll stay away from charged groups
for now). I am not sure how to proceed with polyatomic
molecules in other words. I am thinking that maybe I
have to delve into top->blocks somehow.
Another thing. How can I access basic properties for a
specific atom-type? I have looked and looked for a structure
that does this. Perhaps I should make my own. top->symtab is
not easy to understand. For example, lets say I wish to know
the standard mass and atomname for atom-type 'i'. For the
atomname I would need a formula which converts i into an
address for the corresponding string inside top->symtab.
>Subject: Re: [gmx-developers] dynamic topology
>From: David <spoel at xray.bmc.uu.se>
>To: gmx-developers at gromacs.org
>Date: 25 Oct 2003 10:40:52 +0200
>Reply-To: gmx-developers at gromacs.org
>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
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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