[gmx-users] non squares box

Mark Abraham Mark.Abraham at anu.edu.au
Sun Jun 21 13:33:49 CEST 2009

Omer Markovitch wrote:
> Thanks.
> I am not sure how this addresses my problem. I am getting "broken" 
> structure at the end of the MD (in confout.gro), 

Well, you didn't say you were doing MD. I (and presumably Tsjerk) 
thought you were converting your output from editconf. In such a case, 
Tserk's suggestion lets you tile some boxes together to see how things 
are (not) working. Your results will also depend on the contents of your 
editconf -f file.gro. I suggest you copy and paste your actual commands 
in future :-)


> and want to be sure 
> that GMX treat it correctly during the MD.
>     To check your periodicity use genconf:
>     genconf -f in.pdb -o out.pdb -nbox 2 2 2
> ------------------------------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

More information about the gromacs.org_gmx-users mailing list