[gmx-users] Error after trjconf processing
jmsstarlight at gmail.com
Fri May 3 11:15:39 CEST 2013
thanks for suggestions
as I've told previously I've removed pbc via trjconv witout -pbc mol and -pbc
nojump flags (the same way I found in Justin's umbrella tutorial where
conformers were extracted from pulling trajectory). Might it be source of
the some artifacts with pbc ?
so if I understood correctly subsequent minimization (with maxwarn 1 flag)
restored original pbc (based on box vectors defined in gro file ) because
in next production MD there were no warnings
2013/5/3 Mark Abraham <mark.j.abraham at gmail.com>
> 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
> 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.
> On Fri, May 3, 2013 at 8:18 AM, James Starlight <jmsstarlight at gmail.com
> > 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 #
> > 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
> > 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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