[gmx-users] Constrained MD questions

Arneh Babakhani ababakha at mccammon.ucsd.edu
Tue Aug 29 23:20:00 CEST 2006

Hello GMX Users,

I have some specific questions about the constrained MD run options, as 
explained on page 116 (in the Special Topics section) of the GMX manual.

1.  Regarding "constraint_direction =  "    What exactly is the meaning 
of the 3 values inputted here?  Does 1.0  0.0  0.0  mean the x-axis?  
(If so, why is this not in the "Y N N" format?)  Or are these values 
supposed to be angles?

2.  Also regarding the "constraint_direction", the manual states that if 
left in it's default setting (0.0 0.0 0.0), the distance between groups 
is constrained.  What if you only have one group?  Then is the distance 
between that group and the reference group constrained?

3.  Regarding the "constraint_distance"  The manual states that if left 
in default (= 0), then the distance is determined by the starting 
coordinates.  But what distance are we talking about here? The distance 
between the center-of-mass of the group, and that of the 
reference_group?  For instance, if the center-of-mass of group_1 is 1 nm 
from the COM of the reference_group in the starting coordinates, then 
setting constraint_distance1 = 0  will constrain this distance to 1 nm.  
Is that correct?

4. Is the "pulldim" line necessary, if you're not doing AFM?

Thanks for the help,


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