[gmx-users] Center of mass motion removal

[Alex]

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]
   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.

Thank you
Alex


On Fri, Dec 13, 2019 at 7:50 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/13/19 10:51 AM, Alex wrote:
> > Dallas,
> > Of course that is doable, but removing those flying molecules is not the
> > actual solution specially if one is interested in calculating of some
> > properties in presence of all molecules, rather than visualizing them.
> And
> > also, some other molecules might leave the droplet in some stages, so, by
> > removing those as well, nothing would remain.
>
> Center on a single molecule that ends up near the middle of the cluster.
>
> -Justin
>
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