VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Tue May 24 2016 - 07:40:30 CDT

Dear Norman,
Could you be more specific about how you set up your system? In particular, did you provide an xsc file to set up periodic boundary conditions? The files generated by namdenergy with the debug option on would be ideal. Putting “BUG” in all caps without giving us enough information to reproduce the difficulty that you encountered is not as helpful as it could be.
Best,
Peter

> On May 24, 2016, at 4:02 AM, Norman Geist <norman.geist_at_uni-greifswald.de> wrote:
>
> Dear VMD Developers,
>
> there’s a bug in the Namdenergy feature of VMD causes periodic interactions to not be fully considered. I think it is related to NAMD being started without a box, so NAMD doesn’t initially
> create a valid pairlist. The failure can easily be seen when analyzing a system containing two compounds, that do only meet across pbc boundary. One obtains just zero interaction energies.
>
> Best wishes
>
> Norman Geist