[gmx-users] the box lengths

[#ZHAO LINA#]

________________________________________
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_Convention
>
> -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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