VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu May 07 2009 - 22:45:00 CDT

Could you let us know what version of namd/vmd you're using? Also, if
you used periodic boundary conditions and PME in your simulation, you
should also do so for the postprocessing...
Best,
Peter

BIN ZHANG wrote:
> Dear all:
>
> I met a quite peculiar error while using the NAMDEnergy plugin. I was
> trying to calculate the internal energy of a peptide, and using the
> following command,
>
> set sel1 [atomselect top "chain D"]
> namdenergy -nonb -sel $sel1
>
> I would get a error " bad global exclusion count".
> However, if I use :
> namdenergy -nonb -sel $sel1 $sel1.
> then everything seems to be working fine.
>
> Can anyone explain to me why is this happening? Assuming the second case
> is running correctly, would it twice as large as the first one?
>
> Thanks,
> Bin
>