[gmx-users] Re: Test particle insertion extra coordinate

João M. Damas jmdamas at itqb.unl.pt
Mon Mar 5 01:57:04 CET 2012

The error is correct. After inspecting the code, the extra coordinate
(coordinate of the cavity) is taken from the last atom of the trajectory
(rerun_fr.x) and not from the .tpr file (mdatoms). This is weird, but
allows different cavities for different frames I guess...

I am guessing you can add the extra coordinate (cavity coordinate) to each
frame. You just need to convert from a binary version (.xtc, .trr) to a
ascii version (.gro, .g96), add the coordinate, convert back to binary
(optional, but saves space), and make the rerun over this. Be _careful_
with the conversions not to screw the original trajectory.

Plus, with this, there is no need for topology mambo-jambos (calling CL- to
the cavity location, etc).

I did not remember this because I hacked the code and I bypass that part,
giving the extra coordinate (cavity) through a variable.

I hope this solves your problem.


On Sun, Mar 4, 2012 at 11:54 PM, MPID <mpmcgovern at wisc.edu> wrote:

> Thanks a lot for the reply! I did as you said. I had a coordinate file
> where
> I wanted to add insert a water molecule withing a cavity. I added these
> lines to the .gro file:
>  340SOL     OW 1274   2.925   0.061   2.677  0.2533 -0.1222  0.1294
>  340SOL    HW1 1275   2.893   0.000   2.605 -0.1856  0.5697 -0.2686
>  340SOL    HW2 1276   2.849   0.082   2.739  0.5491 -0.4502  0.6106
>  341INS       X 2036   0.000   0.000   1.000  0.0000  0.0000  0.0000
> I realize I still neeed to center the water molecule, but I am testing now.
> To make grompp work, I added a line in the .top file and called the last
> coordinate a CL- atom. I then can do grompp. But when I do mdrun -rerun, I
> get this error:
> Fatal error:
> Number of atoms in trajectory (2032) minus one is not equal the number in
> the run input file (2036) minus the number of atoms to insert (1)
> The math here seems to imply that the extra atom belongs in the trajectory
> rather than the tpr file, and also, it now thinks I'm inserting a CL- atom
> instead of water.
> --
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João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
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