[gmx-users] gmx trjconv -center not working?

Mala L Radhakrishnan mradhakr at wellesley.edu
Tue Feb 5 20:27:00 CET 2019


Hi again,

As a follow up to my earlier email -- I added -pbc atom to the flags, for a
total command line of:

gmx trjconv -f md.xtc -o md_201000ps.pdb -s md.tpr -b 201000 -e 201000 -n
INDEX.ndx -pbc atom -center

This brought it "closer" to the group I chose being centered, but it is
still not centered at the geometric center of the group I chose.   I'm not
sure why including -pbc atom would make things different from not including
it in this case, either.  Any help would be appreciated.

Mala

On Tue, Feb 5, 2019 at 11:37 AM Mala L Radhakrishnan <mradhakr at wellesley.edu>
wrote:

> Hi,
>
> I am trying to extract snapshots and center on a particular group, but the
> center of the box does not correspond to the geometric center of the group
> as expected.  It is centered on the outer edge of the group.  Here is the
> command I am using:
>
> gmx trjconv -f md.xtc -o md_201000ps.pdb -s md.tpr -b 201000 -e 201000 -n
> INDEX.ndx -center
>
> ...and I then choose the group in the index file that corresponds to what
> I want right in the center; I have verified the correctness of the index
> file.  I ran my simulation with pbc but in this case I specifically want to
> maintain the same cubic box used in the simulations, so I don't want to
> keep molecules whole.  So all I want to do is extract the cubic box that is
> centered on the group I want.   But the resulting snapshot has the molecule
> slightly (about 10%) off center, mainly in the y direction in this case.  I
> presume that center will place the geometric center of the group you choose
> at the geometric center of the box.  Am I incorrect?  Is there another way
> to accomplish what I want?
>
> Thank you so much,
>
> Mala
>
>
> --
> Mala L. Radhakrishnan
> Whitehead Associate Professor of Critical Thought
> Associate Professor of Chemistry
> Wellesley College
> 106 Central Street
> Wellesley, MA 02481
> (781)283-2981
>


-- 
Mala L. Radhakrishnan
Whitehead Associate Professor of Critical Thought
Associate Professor of Chemistry
Wellesley College
106 Central Street
Wellesley, MA 02481
(781)283-2981


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