[gmx-users] Error on Box Length when adding ions (gromacs 4.5.3/Charmm27/Tip3p)

X Rules xrules at live.com
Wed Nov 17 19:44:06 CET 2010

> The error would imply that the box you have set up is < 2.0 nm, given the 
> cutoffs here.  How did you define the box (editconf command)?  What is your box 
> size (last line of the .gro file or in the header of a .pdb)?
> -Justin

okey.. I got it under control. The problem was.

1. created a good box widths.. went upto 30nm with editconf and box vector
2. (Made a mistake while adding ions with genion): saved the file as pdb instead of gro!!
3. was trying grompp with the pdb file (So I have no idea what grommp found different in a file with/witout ions)

Thanks for hinting on the last line of gro. (still I think it is probably a bug or feature)

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101117/44ba3f84/attachment.html>

More information about the gromacs.org_gmx-users mailing list