[gmx-users] Had anybody modied the source code of gromacs

Mark Abraham Mark.Abraham at anu.edu.au
Mon Apr 19 08:04:35 CEST 2010

On 19/04/2010 3:58 PM, 聂雪川 wrote:
> Hello gmx-users,
> I just have one question about modifing the source code of 
> gromacs4.0.7.For I want to control the motion of one certain atom (e.g. 
> atom 200).I added some codes like /"if(n==my_atom)xprime[n][d] = 
> x[n][d]+...;"/ in the functionstatic /void do_update_md()/ of the file/ 
> gromacs-4.0.7\src\mdlib\update.c./But when I run it Parallel (mpi run),I 
> find that the atom serial number n isn't the real atom serial number n 
> on each CPU.So the code /"if(n==my_atom)"/ is futile.How can I achieve it.

The domain decomposition algorithm defines a mapping from the local
state (i.e. subset of topology and atoms) to the global state. You need
to harness that, or don't run in parallel.


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