[gmx-users] pbc atom

[Justin A. Lemkul]

Justin A. Lemkul wrote:
> 
> 
> Gavin Melaugh wrote:
>> Hi all
>>
>> I am generating a series of configurations using the pull code to
>> calculate the pmf. I am using no pbc i.e. pbc =no, howver the output
>> from grommp gives me info on pbc atom.
>>
>> Pull group  natoms  pbc atom  distance at start     reference at t=0
>>        0        72        36
>>        1        72       360   4.290                 4.290
>>
>> why is this so?
>>
> 
> grompp always assigns the numerical middle atom of a group as the PBC 

...unless over-ridden by providing a different value for pbc_pullatom1.

-Justin

> reference point.  In the case of pbc=no, it shouldn't matter.
> 
> http://manual.gromacs.org/current/online/mdp_opt.html#pull
> 
> -Justin
> 
>> Cheers
>>
>> Gavin
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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