[gmx-users] genion doesn't work in 4.6.1?
jalemkul at vt.edu
Fri Apr 5 21:09:19 CEST 2013
On Fri, Apr 5, 2013 at 3:05 PM, Albert <mailmd2011 at gmail.com> wrote:
> I found that there would be some problem of genion in 4.6.1:
> grompp_mpi -f em.mdp -c solv.gro -p complex.top -o ions.tpr
> NOTE 1 [file complex.top, line 44008]:
> System has non-zero total charge: -11.000000
> Total charge should normally be an integer. See
> for discussion on how close it should be to an integer.
> genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -neutral -norandom
> Reading file ions.tpr, VERSION 4.6.1 (single precision)
> Using a coulomb cut-off of 1.2 nm
> No ions to add and no potential to calculate.
> Obviously, the total charge of the system is -11.0, but genion doesn't add
> anything to netural it....
genion has never done anything if you just use -neutral. You need to use
-neutral in conjunction with -conc, otherwise manually specify the number
of ions to add.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540)
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