[gmx-users] genbox job killed

[David van der Spoel]

Wang Zhun wrote:
> Hi,
> 
> Genbox command works well for my previous application: solvation a peptide of 20 AAs on a Compaq AP400 working station(PII400x2,128M). 
> But when I turned to the present job:solvating a protein of 235 AAs, the job was killed. It reads like as below:
> Initialising van der waals distances...
> Will generate new solvent configuration of 12x12x9 boxes
> Generating configuration
> Sorting configuration
> Found 1 molecule type:
>     SOL (   3 atoms): 279936 residues
> Calculating Overlap...
> box_margin = 0.315
> Removed 85908 atoms that were outside the box
> 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
> Generated table with 0 data points for COUL.
> Tabscale = 500 points/nm
> Generated table with 0 data points for LJ6.
> Tabscale = 500 points/nm
> Generated table with 0 data points for LJ12.
> Tabscale = 500 points/nm
> Going to determine what solvent types we have.
> There are 0 molecules, 1006805 charge groups and 1006805 atoms
> There are 0 optimized solvent molecules on node 0
> There are 0 optimized water molecules on node 0
> Grid: 90 x 90 x 63 cells
> Killed
> 
> 
> What's the problem?

Not enough memory in your computer.
Is the protein in extended conformation?

> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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