[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 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.

Thanks,

lina