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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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