________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@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-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf > of Justin A. Lemkul [jalem...@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. > 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 ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
