#ZHAO LINA# wrote:
_______________________________________
From: [email protected] [[email protected]] on behalf
of Justin A. Lemkul [[email protected]]
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
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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