[gmx-users] the box lengths
Justin A. Lemkul
jalemkul at vt.edu
Mon Jun 14 16:07:57 CEST 2010
#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:
>>> 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.
>> 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.
> 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 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
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users