[gmx-users] the box lengths

Dallas B. Warren Dallas.Warren at pharm.monash.edu.au
Tue Jun 15 05:15:46 CEST 2010 

As already mentioned by Justin, unless you copy and paste the commands
and output you got, for us to see, we can only have stabs in the dark
(which is what I did since you are missing lots of information on what
you are actually doing) to what is actually going on.  And don't type in
the commands into your email client, physically go and copy and paste
the text in, otherwise you are filtering it through your own mind.

Go and run the series of commands that work, copy / paste the results
for us to see.

Then go and run the series of commands that don't work, copy / paste
again.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail. 


> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> bounces at gromacs.org] On Behalf Of #ZHAO LINA#
> Sent: Tuesday, 15 June 2010 12:32 PM
> To: Discussion list for GROMACS users
> Subject: RE: [gmx-users] the box lengths
> 
> I used the same commands trying another proteins, but no problems. So
> it's not the reason about the commands I used.
> 
> It did not contain the same number of molecules after genion when I
> changed the box size. The pressure coupling was not on, and I did not
> reach this steps. The problem I had just the steps I did the energy
> minimization after ions (NA+ and CL-) added.
> 
> Thanks and regards,
> 
> lina
> ________________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on
> behalf of Dallas B. Warren [Dallas.Warren at pharm.monash.edu.au]
> Sent: Tuesday, June 15, 2010 6:48 AM
> To: Discussion list for GROMACS users
> Subject: RE: [gmx-users] the box lengths
> 
> Please copy and paste in the commands you are using, and the output.
> 
> I suspect you have made your box bigger, but it still contains the
same
> number of molecules and you still have pressure coupling on. So when
> you
> start the simulation, not surprising that the box compresses again and
> goes under 2nm again.
> 
> Catch ya,
> 
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at pharm.monash.edu.au
> +61 3 9903 9167
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to
> resemble
> a nail.
> 
> 
> > -----Original Message-----
> > From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> > bounces at gromacs.org] On Behalf Of #ZHAO LINA#
> > Sent: Tuesday, 15 June 2010 12:04 AM
> > To: jalemkul at vt.edu; Discussion list for GROMACS users
> > Subject: RE: [gmx-users] the box lengths
> >
> >
> > ________________________________________
> > From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org]
> on
> > behalf of Justin A. Lemkul [jalemkul at vt.edu]
> > Sent: Monday, June 14, 2010 10:02 PM
> > To: Gromacs Users' List
> > Subject: Re: [gmx-users] the box lengths
> >
> > #ZHAO LINA# wrote:
> > > _______________________________________
> > > From: gmx-users-bounces at gromacs.org
[gmx-users-bounces at gromacs.org]
> > on behalf of Justin A. Lemkul [jalemkul at vt.edu]
> > > Sent: Monday, June 14, 2010 9:33 PM
> > > To: Discussion list for GROMACS users
> > > Subject: Re: [gmx-users] the box lengths
> > >
> > > #ZHAO LINA# wrote:
> > >>  Hi,
> > >>
> > >> First time I meet this problem,
> > >> ERROR: One of the box lengths is smaller than twice the cut-off
> > length.
> > >> Increase the box size or decrease rlist.
> > >> I just followed the advice increase the box size, I tried twice
in
> > the
> > >> editconf about the box size, actually this box is really large
> > enough
> > >> for the testing consideration, but still has the same problem.
> > >>
> > >
> > > Well, what are your box vectors?  If they are < 2 nm, you will get
> > this error
> > > because of the minimum image convention.
> > >
> > >
> >
>
http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Conventi
> > on
> > >
> > > -Justin
> > >
> > >     system size :  4.581  2.380  2.715 (nm)
> > >     diameter    :  4.889               (nm)
> > >     center      : -0.012  0.003 -0.904 (nm)
> > >     box vectors :  0.000  0.000  0.000 (nm)
> > >     box angles  :   0.00   0.00   0.00 (degrees)
> > >     box volume  :   0.00               (nm^3)
> > >     shift       :  9.678  9.664  5.461 (nm)
> > > new center      :  9.667  9.667  4.557 (nm)
> > > new box vectors : 12.889 12.889 12.889 (nm)
> > > new box angles  :  60.00  60.00  90.00 (degrees)
> > > new box volume  :1514.05               (nm^3)
> > >
> > > This one I set was really large, but still showed that problems.
> > >
> >
> > What problems?  The same error about the box lengths being shorter
> than
> > twice
> > the cutoff?  I don't think that's possible, given those vectors, if
> > you're
> > keeping your cutoffs at 1.0 nm.
> >
> > -Justin
> >
> > I do keep the cut-off. That's I do not know why. Four times had been
> > tried.
> >
> > > Thanks,
> > >
> > > lina
> > >
> > >
> > >
> >
> > --
> > ========================================
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> > posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> > posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

More information about the gromacs.org_gmx-users mailing list