[gmx-users] totally misunderstood question about genbox

David van der Spoel spoel at xray.bmc.uu.se
Wed Mar 14 08:49:43 CET 2007

> Mark
> I'm sorry--that is not what I was saying at all--I did not have ANY waters originally defined in my .top file. I used editconf to make a cubic box that was 6 x 6 x 6 , then used genbox and in that step specified which topology file in which to insert the waters--a .top file with no water.   Genbox then ilisted a different number of waters at the end of the .top file than what it had put in the .gro file.  I just think it is strange that the program would itself generate two different numbers for the same thing all in one step. 
> Will
if this is reproducible then please submit a bugzilla with exact command 
line and sample input files.

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://folding.bmc.uu.se

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