[gmx-developers] dynamic topology

[Jason DeJoannis]

Hi,

  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[1] 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.

Many thanks,
   -Jason DeJoannis

>Subject: Re: [gmx-developers] dynamic topology
>From: David <spoel at xray.bmc.uu.se>
>To: gmx-developers at gromacs.org
>Organization: 
>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.
>> 
>> 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
>> 
 

---
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