[gmx-users] Re: Distance between Centre of Mass!

Justin Lemkul jalemkul at vt.edu
Tue Oct 9 19:56:59 CEST 2012

Please keep all Gromacs-related correspondence on the gmx-users list.  I am not 
a private tutor.  I am CC'ing this message to the list and will ask that all 
further correspondence be addressed there.

On 10/9/12 12:26 PM, Arman Mahboubi Soufiani wrote:
> Dear Justin,
> I have two layers of PLA and don't know the distance between their centre of
> mass! Moreover, I have to change this distance to specific amount.
> I have made separate indices for all the atoms on the top and bottom layer.
> However, this is the step that I definitely need your direction to adjust the
> correct COM between these two layers of poly(lactic acid).
> I would be greatly thankful if you help me in this regard.

g_dist is the program used to measure distances.  Either you need to place the 
components in your box by specifying their locations with editconf (using 
-translate, -rotate, or -center options as needed) or use the pull code to 
adjust their positions.



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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