[gmx-users] Center of mass motion removal

[Justin Lemkul]

On 12/16/19 12:12 PM, Alex wrote:
> Hi Justin,
>
> Below is the way I understood to center the trajectory on a single
> molecule, would you please confirm if it is true?
>
>
> 1. Adding a new group which contains only the central molecule to the index
> file:
>     a. gmx select -f last-frame.gro -o centeral-mol.ndx ...
>          > resname MOL and within 0.5 of [x,y,z coordinates of center of the
> droplet]

This selection doesn't guarantee that you only get the atoms belonging 
to one molecule.

>     b. gmx trajconv -f last-frame.gro -n centeral-mol.ndx
> -o centeral-mol.gro ....
>
> 2. gmx trajconv -f mol.clust.xtc -n index.ndx -o mol.clust.center.xtc ...
>     Select group for centering
> Group     0 (           Droplet) has  6254 elements
> Group     1 (    centeral-mol) has    45 elements
> Select a group: 1
>
> Select group for output
> Group     0 (           Droplet) has  6254 elements
> Group     1 (    centeral-mol) has    45 elements
> Select a group: 0
>
> And below is the output in which the drifting is bit less but still exist
> and unfortunately the whole droplet moves around:
>
> https://drive.google.com/open?id=1_aVJzfXJQWQ-aP_rHwgEXGeas7KWcnuo
>
> BTW, I used a proper .tpr file where the molecule are all intact.

If the first iteration reasonably approximates centering and you no 
longer have anything drifting off, that should be sufficient for any 
type of analysis, but if you truly require an invariant COM of the 
droplet, follow up with another round of trjconv, centering on the whole 
droplet.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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