<HTML><HEAD></HEAD>
<BODY>
<DIV id=idOWAReplyText72964 dir=ltr>
<DIV dir=ltr><FONT face=Arial color=#000000 size=2>Hi All,</FONT></DIV>
<DIV dir=ltr><FONT face=Arial size=2></FONT> </DIV>
<DIV dir=ltr><FONT face=Arial size=2>I am still having problem with pure decane box. Still crashing with constrain ( all-bonds). I have been wondering why this is happening?</FONT></DIV>
<DIV dir=ltr><FONT face=Arial size=2></FONT> </DIV>
<DIV dir=ltr><FONT face=Arial size=2>With regards,</FONT></DIV>
<DIV dir=ltr><FONT face=Arial size=2></FONT> </DIV>
<DIV dir=ltr><FONT face=Arial size=2>Abu</FONT></DIV></DIV>
<DIV dir=ltr><BR>
<HR tabIndex=-1>
<FONT face=Tahoma size=2><B>From:</B> David van der Spoel<BR><B>Sent:</B> Mon 29/08/2005 17:53<BR><B>To:</B> Discussion list for GROMACS users<BR><B>Subject:</B> Re: [gmx-users] Decane<BR></FONT><BR></DIV>
<DIV><PRE style="WORD-WRAP: break-word">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@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@gromacs.org.
> >> >>
> >> >>
> >> >
> >> > _______________________________________________
> >> > gmx-users mailing list
> >> > gmx-users@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@gromacs.org.
> >> >
> >>
> >>
> >>
> >> __________________________________________________________________
> >>
> >> DISCLAIMER:
> >>
> >> This e-mail message is subject to http://www.hw.ac.uk/disclaim.htm
> >> __________________________________________________________________
> >>
> >> _______________________________________________
> >> gmx-users mailing list
> >> gmx-users@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@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@xray.bmc.uu.se spoel@gromacs.org http://xray.bmc.uu.se/~spoel
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users@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@gromacs.org.
> >
>
>
>
> __________________________________________________________________
>
> DISCLAIMER:
>
> This e-mail message is subject to http://www.hw.ac.uk/disclaim.htm
> __________________________________________________________________
>
> _______________________________________________
> gmx-users mailing list
> gmx-users@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@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@xray.bmc.uu.se spoel@gromacs.org http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list
gmx-users@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@gromacs.org.
</PRE></DIV></BODY></HTML>