From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Fri Mar 13 2015 - 09:42:21 CDT
You're right, it should not be affected by water. Something else must have
gone wrong.
Jerome
On 13 March 2015 at 15:25, Kevin C Chan <cchan2242-c_at_my.cityu.edu.hk> wrote:
> Here I return with successful consistent colvar.traj from
> off-wrapping-output simulations. Thanks so much for the valuable comments
> and credits to Jerome.
>
> But I still have one follow-up question: As I observe from both wrapped or
> un-wrapped trajectories, in none of them the protein was having large
> translational moves, not mentioning crossing the pbc boundaries. So for my
> understanding, only the water molecules are wrapped then why would my
> colvars calculations of dihedral angles be affected?
>
> Regards,
> Kevin
>
> On 12 Mar, 2015, at 19:29, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
>
>
>> 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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