[gmx-users] gmx_dipoles Mtot and aver difference

[Justin Lemkul]

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

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

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340 West Campus Dr.
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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