[gmx-users] Error after trjconf processing

[Mark Abraham]

Trajectory frames written by mdrun are not post-processed to guess how you
would like PBC to be treated for whatever purpose you have next. So if a
molecule straddles a periodic boundary given the current center position,
that's what it looks like. If there are things you want to do, then there's
the instructions at
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
.

In turn, it seems grompp applies a whole collection of basic checks, and it
seems that one of them might not be sufficiently PBC-aware. Such checks
appropriate for a normal grompp workflow, where this is the first point the
GROMACS machinery gets to see what you intend to do and is the point where
it can help you ensure sanity. It seems there's room for a small
improvement, too.

If the subsequent MD works, then you need have no concern, but if you want
to post-process your trjconv frames so that the molecules are whole, you
will suppress this warning the "correct" way.

Mark

On Fri, May 3, 2013 at 8:18 AM, James Starlight <jmsstarlight at gmail.com>wrote:

> Dear Gromacs users!
>
> I have performed long md run. From the production trajectory by means of
>
> trjconv -f md_.trr -s cam.tpr  -dt 10 -e 300 -sep -o ./pdbs/.pdb  # extract
> conformers from first 300 ps each 10ps steps
>
>
> I've extracted 10 conformers in the desired time step
>
> Than when I perform MD on each conformer I obtain error (when I loaded in
> grompp  conformer from the initial run I have no such error)
>
> Number of degrees of freedom in T-Coupling group rest is 130551.00
> Largest charge group radii for Van der Waals: 8.895, 7.586 nm
> Largest charge group radii for Coulomb:       8.895, 8.474 nm
>
> WARNING 1 [file ./mdps/minim.mdp]:
>   The sum of the two largest charge group radii (17.368397) is larger than
>   rlist (1.000000)
>
>
> Finally after minimization of each conformer with the same R_list (with
> maxwarn 1 flag) and starting new MD on the minimizing conformer I have no
> such error:
> Largest charge group radii for Van der Waals: 0.241, 0.237 nm
> Largest charge group radii for Coulomb:       0.241, 0.237 nm
>
> Why this error have occurred (with no minimized conformers) and how it
> could be fixed correctly ?
>
> James
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