[gmx-users] The problems of controling one atom through modifygromacs sourse code

Carsten Kutzner ckutzne at gwdg.de
Thu Apr 22 09:54:22 CEST 2010

Hi Chuan,

you might want to take a look at gmx_ga2la.h. The function
ga2la_home provides the local atom number for a given global
atom number (or returns FALSE if the atom is not found on the local


On Apr 21, 2010, at 4:40 PM, 聂雪川 wrote:

> Hi,gmx-users,
>    Now I want to control the motion of a certain atom (due to special needs).So 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 mpi run,The gromacs performs a domain decomposition algorithm ,which assign  a certain amount of atoms to each CPU(The atoms called local atoms).But the serial number "n" of local atoms always start from 0.So the code "if(n==my_atom)" is futile.
>    Now I come into consideration to differentiate "my_atom" by its name.But I am not sure about whether there exist the atom name at the the process of mdrun.Or Is there a more simple way to  achieve it.
> {The functions be involved with domain decomposition algorithm are:
> /src/mdlib/domdec.c(7458) void dd_partition_system()  (called by do_md())
> /src/mdlib/domdec.c(3365) static void get_cg_distribution()
> /src/mdlib/domdec_network.c(187)void dd_scatter()
> }
>                                                               Thank your.
>                                                                   chuan
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Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302

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