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
--
========================================
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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