[gmx-users] System killed after genbox

Nur Syafiqah Abdul Ghani pqah123 at gmail.com
Wed Dec 19 03:47:15 CET 2012

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

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?

the formula is

no.of molecule that need =( [ % need of hfi x density kg/m^3 x size of
box m^3] / molecular weight g/mol ) x avogadro number

Best Regards,

Nur Syafiqah Abdul Ghani,
Theoretical and Computational Chemistry Laboratory,
Department of Chemistry,
Faculty of Science,
Universiti Putra Malaysia,
43400 Serdang,
alternative email : syafiqahabdulghani at gmail.com

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