From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Thu Mar 12 2015 - 06:29:22 CDT
>
>
> So do you mean that NAMD reads in a coordinate (either pdb or coor) and do
> no wrapping before a simulation?
Exactly.
> I thought it does or we will have trouble that feeding a wrapped coor or a
> unwrapped one would be different.
>
The physics is exactly the same as long as you only have pair interactions
that follow the minimum image convention. The only place where it makes a
difference is for collective variables for which the minimum image
convention doesn't work. Then it is your responsibility to provide NAMD
with initial coordinates in which that the variable is properly defined.
> I will try turning off wrap options in NAMD and try all things again see
> whether we will have consistent results.
>
Yup.
Best,
Jerome
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