[gmx-users] Problem with -shell parameter of genbox

Nicolas Michel n.michel84 at wanadoo.fr
Tue Aug 13 20:28:03 CEST 2002

Hello everybody,
I try to use the MS-Windows port of Gromacs 3.1.2 by E. Lindahl on my own
system: a non-natural lipid. I encounter problem using the -shell parameter
of genbox: I begin with a single lipid in order to test the forcefield... I
convert my initial pdb file with editconf with modification of the box in
order to have a distance of 0.5 between the solute and the box and to align
the principal axe of my lipid (-princ) - this looks fine working.
Then I try to generate a box of solvent directly on the polar head of my
lipid - the system crashes.
If I ommit the -shell parameter, all goes well and I get a fully hydrated
Is there someone who could tell me where I am wrong (is it a bad
manipulation or a bug relative to windows me)?
Thanks in advance

Nicolas Michel
Doctorant en Chimie Organique
Laboratoire de Chimie BioOrganique et des Systemes Moleculaires =

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