[gmx-users] (no subject)

[Justin A. Lemkul]

saly jackson wrote:
> Hi,
> 
> I want to add 80000 of a molecule including 6 atoms. But when I run each 
> of the following commands I
> 
> System total charge: 0.000
> Grid: 5 x 5 x 5 cells
> nri = 1948, nrj = 22927
> Try 63309box_margin = 3t overlap:
> Neighborsearching with a cut-off of 3
> Table routines are used for coulomb: FALSE
> Table routines are used for vdw:     FALSE
> Cut-off's:   NS: 3   Coulomb: 3   LJ: 3
> System total charge: 0.000
> Grid: 5 x 5 x 5 cells
> nri = 1946, nrj = 22921
> Try 63310box_margin = 3t overlap:
> Neighborsearching with a cut-off of 3
> Table routines are used for coulomb: FALSE
> Table routines are used for vdw:     FALSE
> Cut-off's:   NS: 3   Coulomb: 3   LJ: 3
> System total charge: 0.000
> Grid: 5 x 5 x 5 cells
> nri = 1930, nrj = 22871
> Try 63311box_margin = 3t overlap:
> Neighborsearching with a cut-off of 3
> Table routines are used for coulomb: FALSE
> Table routines are used for vdw:     FALSE
> Cut-off's:   NS: 3   Coulomb: 3   LJ: 3
> System total charge: 0.000
> Grid: 5 x 5 x 5 cells
> nri = 1930, nrj = 22911
> Try 63312box_margin = 3t overlap:
> Neighborsearching with a cut-off of 3
> Table routines are used for coulomb: FALSE
> Table routines are used for vdw:     FALSE
> Cut-off's:   NS: 3   Coulomb: 3   LJ: 3
> System total charge: 0.000
> Grid: 5 x 5 x 5 cells
> nri = 1930, nrj = 22885
> Try 63313box_margin = 3t overlap:
> Neighborsearching with a cut-off of 3
> Table routines are used for coulomb: FALSE
> Table routines are used for vdw:     FALSE
> Cut-off's:   NS: 3   Coulomb: 3   LJ: 3
> System total charge: 0.000
> Grid: 5 x 5 x 5 cells
> nri = 1935, nrj = 22846
> Try 63314box_margin = 3t overlap:
> Neighborsearching with a cut-off of 3
> Table routines are used for coulomb: FALSE
> Table routines are used for vdw:     FALSE
> Cut-off's:   NS: 3   Coulomb: 3   LJ: 3
> System total charge: 0.000
> Grid: 5 x 5 x 5 cells
> nri = 1936, nrj = 22827
> Try 63315box_margin = 3t overlap:
> Neighborsearching with a cut-off of 3
> Table routines are used for coulomb: FALSE
> Table routines are used for vdw:     FALSE
> Cut-off's:   NS: 3   Coulomb: 3   LJ: 3
> System total charge: 0.000
> Grid: 5 x 5 x 5 cells
> nri = 1930, nrj = 22863
> Try 63316box_margin = 3t overlap:
> Neighborsearching with a cut-off of 3
> Table routines are used for coulomb: FALSE
> Table routines are used for vdw:     FALSE
> Cut-off's:   NS: 3   Coulomb: 3   LJ: 3
> System total charge: 0.000
> Killed
> 

You haven't shown your actual comment, but I assume it's some form of genbox -ci 
-nmol.  This is a rather impractical approach to adding such a large amount of 
molecules, as your system's memory may get exhausted, which I suspect is the 
case here.

The better approach is to use genconf -nbox to generate a suitable grid of a 
smaller number of molecules, say a few hundred, then use genbox -cs -maxsol to 
fill a new box with the desired number of solvent molecules.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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