[gmx-users] trjconv -pbc

[Justin A. Lemkul]

Carla Jamous wrote:
> Hi everyone,
> 
> please I'm doing a simulation of a dimer with a ligand.
> 
> When I want to visualize my trajectory, I have the problem that my dimer 
> or my ligand or both diffuse out of the box and I don't have a 
> continuous trajectory.
> 
> I tried many options:
> 
> 1)trjconv -center -pbc mol -ur compact (centering on protein)
> 
> 2) trjconv -center -pbc mol (centering on the ligand)
> 
> 3) trjconv -center -pbc atom (centering on ligand)
>     and then, trjconv -pbc whole
> 
> 4) trjconv -pbc nojump
>     and then trjconv -fit rot+trans
> 
> 5) trjconv -center -pbc mol (centering on protein)
>     and then trjconv -fit rot+trans
> 
> 6) trjconv -center -pbc mol -ur compact (centering on ligand)
>     and then -fit rot+trans
> 
> _all of these options didn't work_
> 
> I tried a last one:
> 
> trjconv -center -pbc atom -ur compact (centering on ligand)
> and then trjconv -pbc nojump
> and then trjconv -fit rot+trans
> 
> this one is the best one but I still have one part of my molecule that 
> diffuses out of the box at one point in my trajectory.
> 
> Please I'm out of ideas, can anyone give me a hint on how to get a fully 
> continuous trajectory entirely centered in my box?
> 

Make a custom index group that corresponds to a residue (or several) at the 
dimer interface.  Then use that group for centering.  It still make take a 
couple of passes through trjconv, but I would think that trjconv -pbc mol 
-center would probably work in this case.

-Justin

> Thank you
> 
> Carla
> 

-- 
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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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