[gmx-users] Decane

[Naser, Md Abu]

Hi All,

I am still having problem with pure decane box. Still crashing with constrain ( all-bonds). I have been wondering why this is happening?

With regards,

Abu



From: David van der Spoel
Sent: Mon 29/08/2005 17:53
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Decane


On Mon, 2005-08-29 at 17:41 +0100, M.Naser wrote:
> Hi David,
> 
> Yes, it was inside the box. I going to try with genconf.
the box needs to be 0.4 nm larger than the molecule in all dimensions to
prevent bad contacts.
> 
> With regards,
> 
> Abu
> 
> > 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
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> >
> > _______________________________________________
> > 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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


_______________________________________________
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.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20050831/82f1bcdd/attachment.html>