[gmx-users] tpr file for trjconv command

[Justin A. Lemkul]

ana johari wrote:
> Dear user,
> 
> During simulation I restart the Md run and know I have two .tpr file. 
> Because my molecule split over boundary after 1 ns of simulation,I want 
> to use “trjconv” as a command to center my molecule but I don’t know to 
> chose my first tpr file( for the first 1ns) or the second one after 
> restarting.

Use the first one, which I've said at least twice now.  Think about what you're 
trying to achieve - some sort of fitting to a reference structure such that the 
protein stays in some convenient (but ultimately, arbitrary) location.

If you start with a protein properly centered within the box (at time zero, i.e. 
the state in the first .tpr file), then that's a sensible reference, is it not? 
  It is possible to fit to whatever reference you wish, any intermediate frame 
or other .tpr file, but if you're not comfortable with these concepts yet, do 
what is most intuitive and fit to your starting state.  Doing so will produce a 
smooth trajectory that you can visualize very easily.

-Justin

> 
> Tanks
> 
>  
> 

-- 
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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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