[gmx-users] pbc atom

[Justin A. Lemkul]

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 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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