AMBER Archive (2009)

Subject: Re: [AMBER] problem with energy calculations

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Jul 10 2009 - 12:25:56 CDT

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_at_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
>
>
>
>
>
>
>
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