[gmx-developers] How to get some data from t_state (data structure)?

Mark Abraham mark.abraham at anu.edu.au
Wed Mar 16 09:42:33 CET 2011

On 16/03/11, Yukun Wang  <wangykoo at gmail.com> wrote:
> Hi all:
>       T_state contains almost all of the non-static state of the system including  position, velocity and charge group data  for the home atoms. Before running I defined a new group  which includes all the atoms interested by command make_ndx and grompp, for some purpose I need to know this new group's dynamical information, for examples every atom's position.
>       I know these information must be in the t_state structure, however, I just don't konw how to get them out by self-defined group. Do you have any ideas? Thank you very much! 

You should probably use the user-group .mdp option (see manual 7.3) to make grompp pass the group from the -n file to mdrun. To see how to use the group, have a look at how the XTC output group is used, since that does much the same thing you want to do. Note that the different parallelization schemes available will make your life awkward.

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