[gmx-users] gmx_dipoles Mtot and aver difference

Justin Lemkul jalemkul at vt.edu
Sun Aug 26 13:54:13 CEST 2018

On 8/26/18 12:44 AM, Raag Saluja wrote:
> I gave the following commands:
> gmx_mpi trjconv -s md.tpr -f md.xtc -o md_noPBC.xtc -pbc mol -center (I
> first selected 0 and then 1, like in the lysoyme tutorial).
> gmx_mpi dipoles -f md_noPBC.xtc -s md.tpr
> Despite that, I am getting opposite values in Mtot and aver. By re-center
> do you mean something other than that?

Yes, as David said as well, you need to place the center-of-charge (not 
center-of-mass) at the coordinate origin (not the center of the box) and 
there is no GROMACS tool that does this. You'll have to code something 
up yourself.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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