[gmx-users] genion doesn't work in 4.6.1?

[Justin Lemkul]

On Fri, Apr 5, 2013 at 3:05 PM, Albert <mailmd2011 at gmail.com> wrote:

> Hello:
>
>  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
>   http://www.gromacs.org/**Documentation/Floating_Point_**Arithmetic<http://www.gromacs.org/Documentation/Floating_Point_Arithmetic>
>   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

-- 

========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================