From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Mar 13 2015 - 10:05:20 CDT
Hello Kevin it would be good if you could upload a set of test input files
to github.com/colvars, so that we can investigate the possibility of a bug
in the code. Would that be possible?
Giacomo
On Mar 13, 2015 3:43 PM, "Jérôme Hénin" <jerome.henin_at_ibpc.fr> wrote:
> 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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