[gmx-users] Decane

[David van der Spoel]

On Mon, 2005-08-29 at 17:30 +0100, M.Naser wrote:
> Hi Erik,
> 
> Thanks for your reply. I was trying to get a decane box of 730kg/cm^3. I
> started with dec50.gro file from the pakage. I took just one molecule from
> the file and put the molecule in reletively bigger box that is 2 2 2 nm
> using editconf to avoid bad contact. Then, using genbox I fill a box of 30
> 30 10 nm with the decane molecule. Then I run mdrun using pressure couple
> to get the desired density. When I run with constraint after a few ps run,
> it starts producing a lot of pdb files but when I run with no constrain it
> woks perfectly well. By the way, I have  tried with both algorithm : SHAKE
> and LINCS.
is the decane molecule completely inside the 2 2 2 box?
You may want to use genconf rather than genbox.
> 
> With regards,
> 
> Abu
> 
> > Hi,
> >
> > That's impossible to say without more information - please post the
> > explicit error message!
> >
> > Cheers,
> >
> > Erik
> >
> > On Aug 29, 2005, at 5:40 PM, M.Naser wrote:
> >
> >> Hi All,
> >>
> >> I have been wondering why my simulation of decane crashing with all-
> >> bond
> >> constrain?
> >>
> >> Thanks in advance,
> >>
> >> Abu
> >>
> >>
> >> __________________________________________________________________
> >>
> >> DISCLAIMER:
> >>
> >> This e-mail message is subject to http://www.hw.ac.uk/disclaim.htm
> >> __________________________________________________________________
> >>
> >> _______________________________________________
> >> gmx-users mailing list
> >> gmx-users at gromacs.org
> >> http://www.gromacs.org/mailman/listinfo/gmx-users
> >> Please don't post (un)subscribe requests to the list. Use the
> >> www interface or send it to gmx-users-request at gromacs.org.
> >>
> >>
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> >
> 
> 
> 
> __________________________________________________________________
> 
> DISCLAIMER:
> 
> This e-mail message is subject to http://www.hw.ac.uk/disclaim.htm
> __________________________________________________________________
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++