[gmx-users] question about define groups

Justin Lemkul jalemkul at vt.edu
Fri Dec 28 14:19:01 CET 2012

On 12/27/12 8:44 PM, yeqing1211 wrote:
> Hello everyone:
>         I prepar to make a QM/MM simulation by employing gromacs compiled
> with mopac, and need to define two groups which are treated by QM and MM
> separately, the question is this: during the dynamics course of my research
> system, particles will enter/leave the QM zone, so there is a
> changing-particle-number situation in the QM zone, I checked the information
> about command "make_ndx", which seems define a group by atom type, name, or
> residue and so on, but in my situation I need to define a group by space,
> namely define all atoms have a distance from a fixed coordinate shorter than
> a given radii as a QM group while the rest atoms are defined as MM group
> (the group members will change during the dynamic course), but I don't know
> whether "make_ndx" can achieve this purpose? If can not, is there any other
> methods can define groups by space?

The group chosen as the QM subset is fixed.  It is defined once (in the .mdp 
file) and the group is created by make_ndx.  I don't think there is anything 
within mdrun that will allow for a dynamic change in the group's contents.

The g_select program allows you to specify geometric criteria for creating 
groups based on each frame of an existing trajectory, but this has no relevance 
to your problem, because you would need mdrun to detect changes in the group.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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