[gmx-users] gmx_dipoles Mtot and aver difference
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
Justin A. Lemkul, Ph.D.
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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