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

[Anton Feenstra]

Anton Feenstra wrote:
> 
> Nicolas Michel wrote:
> >
> > 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
> > system!
> > 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
> 
> Putting a shell of spc around a single arginine works for me, but that
> is on a SGI machine. I'll try it on MSW later...

Works like a charm on my laptop using MS-W2K and the binary Gromacs
distribution from the website... Could you explain exactly what you
did and perhaps copy over the exact error message(s) you got?

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
| |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
| |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
|  /  \  |-----------------------------------------------------------|
| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
|  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
|   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
|  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
| (    ) |-----------------------------------------------------------|
|  \__/  | "Uh-oh, We're In Trouble" (Shampoo)                       |
|________|___________________________________________________________|