[gmx-users] the box lengths

Justin A. Lemkul jalemkul at vt.edu
Tue Jun 15 04:42:06 CEST 2010 


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

The problem is not whether or not your commands work for other systems, rather 
the fact that they are (for some reason) not working for this particular system. 
  Most standard commands work just fine.  The reason I asked originally was to 
see exactly what your commands were to check if you were using the right files 
instead of accidentally repeating the commands on the coordinate file with the 
improper box vectors.

That is also (I suspect) the reason Dallas asked for you to copy and paste all 
your commands.

We can't get inside your head to see what you're doing, so if you want free 
help, you need to provide the information we ask for so we can quickly resolve 
this.  If grompp is still complaining about box vectors, you're either using the 
wrong coordinate file, or you've somehow managed to mangle the coordinate file 
format.  Without seeing your actual commands and any other relevant details, the 
best anyone can offer is "you're doing something wrong."

-Justin

> 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
>>
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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

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