[gmx-users] System killed after genbox

[Justin Lemkul]

On 12/18/12 9:47 PM, Nur Syafiqah Abdul Ghani wrote:
> Dear Users,
>
> Why I run the command genbox -cp protein_box.gro -ci hfi.gro -nmol
> 1534 -cs spc216.gro -p control.top -o protein_mixsol.gro.
>
> And the result show like below.:
>
>
> Grid: 15 x 15 x 11 cells
> nri = 9466, nrj = 77062
> Try 9579box_margin = 0.45overlap:
> Neighborsearching with a cut-off of 0.48
> Table routines are used for coulomb: FALSE
> Table routines are used for vdw:     FALSE
> Cut-off's:   NS: 0.48   Coulomb: 0.48   LJ: 0.48
> System total charge: 0.000
> Killed
>
>
> I already calculate the amount of no of molecule that I need to put
> for the co-solvent.
>
> Is there something wrong of my calculation?
>

You're doing too many things at once and running out of memory.  Add your 
co-solvent with -ci -nmol, then in a separate step add water with -cs.

-Justin

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

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