[gmx-users] shift in trajectory

[Justin Lemkul]

On 10/16/19 11:53 AM, Patel, Lara Anne wrote:
> Have you tried using the -center flag with -pbc mol for example:
>
>
> gmx trjconv -f traj.xtc -o traj-centered.xtc -center -pbc mol -n index.ndx
>
>
> The reason to give the index file is so that you can select the group that you are centering by.  If you do not have the residue's A as a seperate group in the index file, you should start by producing an index file with your centering group isolated and then another group for what you will want to be printing in your new trajectory file.
>
>
> There is one small caveate to the centering algorithm though: There are two ways that the center of mass of an object can be in the middle of the simulation box.
>
>    1) The mass is in the center of the box.
>
>    2) The mass is split on opposite ends of the box.
>
> The last time I was using the -center function of the trjconv function, it would alternate between the two. I am not sure if this has been fixed.

trjconv doesn't choose; it simply computes the center based on 
coordinates you provide. That's why step 1 in the suggested workflow in 
the manual is "make molecules whole." That way, there is no issue with 
placing the atoms in the center.

-Justin

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Justin A. Lemkul, Ph.D.
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