[gmx-users] the box lengths

[Justin A. Lemkul]

#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 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. 
> 

Are you using the right files?  You're not repeating the same commands with the 
zero-box length vectors (which was the source of your problem in the first 
place)?  There is absolutely no reason you'd get an error with 1.0-nm cutoffs 
and > 12 nm box vectors.

-Justin

>> 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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-- 
========================================

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

========================================