[gmx-users] the box lengths

Mark Abraham mark.abraham at anu.edu.au
Tue Jun 15 04:44:43 CEST 2010 


----- Original Message -----
From: #ZHAO LINA# <ZHAO0139 at e.ntu.edu.sg>
Date: Tuesday, June 15, 2010 12:34
Subject: RE: [gmx-users] the box lengths
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> I used the same commands trying another proteins, but no 
> problems. So it's not the reason about the commands I used.

Whether the commands work on some presumably-larger system is not the issue. The way the contents of your *small* system interact with your commands is the issue. You are describing anomalous behaviour. That's probably because you're doing something wrong, so we want to see your actual command lines and output to help you learn why this is happening. Accordingly, we're not all that interested in things that have been filtered through your head :-) If the current knowledge in your head was accurate, you wouldn't be needing help :-)

Mark

> 
> 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 
> resemblea 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
> >
> > ========================================
> > --
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