[gmx-users] trajectory output from g_select ?

Mark Abraham Mark.Abraham at anu.edu.au
Fri Mar 4 08:05:07 CET 2011

On 4/03/2011 11:01 AM, jkhao at ifr88.cnrs-mrs.fr wrote:
> Hi,
> I'm using g_select ( great tool !) to isolate a series of identical 
> molecules, and I need to run some gmx analyses of heavy trajectories.
> If the number of molecules selected is constant over all the frames, 
> it's possible to rebuild a trajectory from the output index and 
> g_traj. The problem is that the extraction needs to call g_traj as 
> much as there's index groups (at least one index group for each 
> frame), so it's not verry efficient for large trajectories.
> Is there a way to do that more efficiently ?

I'm not very clear on what you're trying to do. You have different sets 
of atoms you need to extract from different trajectory frames according 
to some criterion expressed with g_select? Why do you need g_traj? Does 
splitting the trajectory into frames with trjconv help?


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