why are you getting virtual box energies in the gas phase? is the system
really periodic?
On Fri, Jul 10, 2009 at 12:13 PM, Thomas Lake
<thomas.lake08.imperial.ac.uk>wrote:
> Hello,
>
> I have been modelling a peptide and am trying to carry out energy
> calculations of it in the gas-phase. For this I use the mm_pbsa script,
> but using only MM.
>
> I am able to calculate the energy of just the peptide. However when I
> include counterions (but no solvent), I get an error message:
>
> 'The system has extended beyond the extent of virtual box'
>
> If I do reimaging of the trajectory (image center familiar) then I dont
> get this error message. However the energies that are calculated give
> very high vdW energies for certain frames. This I think is because
> counterions have come into close contact in these frames.
>
> I cannot think of any more possible solutions for this, so wandering if
> anyone help me.
>
> Regards
>
> Thomas Lake
> Imperial College London
>
>
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jul 11 2009 - 01:07:17 PDT
